X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details Well solution consisted of 20% PEG 3350, 0.1M potassium nitrate. 1uL of well solution was mixed with 1uL protein solution (10mg/mL) and equilibrated over 500uL well solution., pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.72 α = 90
b = 108.3 β = 99.92
c = 69.06 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2004-12-16
Diffraction Radiation
Monochromator Protocol
Si(111) Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.96411 APS 23-ID-B

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.1 20 93.9 0.052 0.052 -- 3.6 40957 40957 0.0 0.0 34.16
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.1 2.17 84.9 0.406 0.406 2.7 3.1 3686

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.1 19.203 0.0 0.0 38758 38758 1896 88.75 -- -- 0.173 0.221 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.1 2.109 335 -- 335 0.291 -- -- 57.0
X Ray Diffraction 2.109 2.119 373 -- 373 0.302 -- -- 65.0
X Ray Diffraction 2.119 2.129 415 -- 415 0.269 -- -- 69.0
X Ray Diffraction 2.129 2.139 423 -- 423 0.266 -- -- 73.0
X Ray Diffraction 2.139 2.149 424 -- 424 0.269 -- -- 70.0
X Ray Diffraction 2.149 2.16 415 -- 415 0.25 -- -- 70.0
X Ray Diffraction 2.16 2.171 411 -- 411 0.259 -- -- 72.0
X Ray Diffraction 2.171 2.181 427 -- 427 0.247 -- -- 73.0
X Ray Diffraction 2.181 2.193 420 -- 420 0.245 -- -- 74.0
X Ray Diffraction 2.193 2.204 465 -- 465 0.235 -- -- 77.0
X Ray Diffraction 2.204 2.215 426 -- 426 0.224 -- -- 76.0
X Ray Diffraction 2.215 2.227 472 -- 472 0.22 -- -- 75.0
X Ray Diffraction 2.227 2.239 390 -- 390 0.222 -- -- 69.0
X Ray Diffraction 2.239 2.252 452 -- 452 0.231 -- -- 75.0
X Ray Diffraction 2.252 2.264 476 -- 476 0.225 -- -- 81.0
X Ray Diffraction 2.264 2.277 431 -- 431 0.2 -- -- 77.0
X Ray Diffraction 2.277 2.29 440 -- 440 0.195 -- -- 76.0
X Ray Diffraction 2.29 2.304 476 -- 476 0.206 -- -- 78.0
X Ray Diffraction 2.304 2.318 447 -- 447 0.19 -- -- 76.0
X Ray Diffraction 2.318 2.332 457 -- 457 0.19 -- -- 80.0
X Ray Diffraction 2.332 2.346 456 -- 456 0.177 -- -- 76.0
X Ray Diffraction 2.346 2.362 463 -- 463 0.17 -- -- 79.0
X Ray Diffraction 2.362 2.377 491 -- 491 0.171 -- -- 81.0
X Ray Diffraction 2.377 2.392 459 -- 459 0.178 -- -- 80.0
X Ray Diffraction 2.392 2.409 454 -- 454 0.172 -- -- 81.0
X Ray Diffraction 2.409 2.425 476 -- 476 0.158 -- -- 80.0
X Ray Diffraction 2.425 2.442 468 -- 468 0.175 -- -- 80.0
X Ray Diffraction 2.442 2.46 500 -- 500 0.18 -- -- 79.0
X Ray Diffraction 2.46 2.478 470 -- 470 0.165 -- -- 82.0
X Ray Diffraction 2.478 2.496 483 -- 483 0.17 -- -- 85.0
X Ray Diffraction 2.496 2.516 483 -- 483 0.159 -- -- 83.0
X Ray Diffraction 2.516 2.535 486 -- 486 0.168 -- -- 82.0
X Ray Diffraction 2.535 2.556 492 -- 492 0.19 -- -- 83.0
X Ray Diffraction 2.556 2.577 487 -- 487 0.185 -- -- 82.0
X Ray Diffraction 2.577 2.599 508 -- 508 0.186 -- -- 86.0
X Ray Diffraction 2.599 2.621 507 -- 507 0.174 -- -- 86.0
X Ray Diffraction 2.621 2.645 473 -- 473 0.167 -- -- 84.0
X Ray Diffraction 2.645 2.669 532 -- 532 0.186 -- -- 87.0
X Ray Diffraction 2.669 2.694 491 -- 491 0.188 -- -- 85.0
X Ray Diffraction 2.694 2.72 521 -- 521 0.176 -- -- 84.0
X Ray Diffraction 2.72 2.747 512 -- 512 0.174 -- -- 89.0
X Ray Diffraction 2.747 2.775 517 -- 517 0.179 -- -- 88.0
X Ray Diffraction 2.775 2.805 507 -- 507 0.202 -- -- 88.0
X Ray Diffraction 2.805 2.835 519 -- 519 0.188 -- -- 88.0
X Ray Diffraction 2.835 2.868 526 -- 526 0.186 -- -- 87.0
X Ray Diffraction 2.868 2.901 511 -- 511 0.175 -- -- 90.0
X Ray Diffraction 2.901 2.936 527 -- 527 0.165 -- -- 89.0
X Ray Diffraction 2.936 2.973 524 -- 524 0.186 -- -- 90.0
X Ray Diffraction 2.973 3.012 553 -- 553 0.183 -- -- 91.0
X Ray Diffraction 3.012 3.053 548 -- 548 0.191 -- -- 91.0
X Ray Diffraction 3.053 3.097 535 -- 535 0.179 -- -- 93.0
X Ray Diffraction 3.097 3.143 536 -- 536 0.171 -- -- 91.0
X Ray Diffraction 3.143 3.192 561 -- 561 0.167 -- -- 94.0
X Ray Diffraction 3.192 3.244 551 -- 551 0.183 -- -- 93.0
X Ray Diffraction 3.244 3.3 530 -- 530 0.183 -- -- 93.0
X Ray Diffraction 3.3 3.359 552 -- 552 0.167 -- -- 93.0
X Ray Diffraction 3.359 3.424 565 -- 565 0.166 -- -- 92.0
X Ray Diffraction 3.424 3.493 530 -- 530 0.164 -- -- 94.0
X Ray Diffraction 3.493 3.569 567 -- 567 0.148 -- -- 94.0
X Ray Diffraction 3.569 3.651 568 -- 568 0.166 -- -- 94.0
X Ray Diffraction 3.651 3.742 549 -- 549 0.161 -- -- 94.0
X Ray Diffraction 3.742 3.842 546 -- 546 0.152 -- -- 94.0
X Ray Diffraction 3.842 3.954 556 -- 556 0.142 -- -- 93.0
X Ray Diffraction 3.954 4.081 559 -- 559 0.149 -- -- 94.0
X Ray Diffraction 4.081 4.225 550 -- 550 0.147 -- -- 94.0
X Ray Diffraction 4.225 4.392 566 -- 566 0.144 -- -- 94.0
X Ray Diffraction 4.392 4.589 565 -- 565 0.129 -- -- 94.0
X Ray Diffraction 4.589 4.828 540 -- 540 0.132 -- -- 94.0
X Ray Diffraction 4.828 5.125 581 -- 581 0.145 -- -- 95.0
X Ray Diffraction 5.125 5.512 550 -- 550 0.167 -- -- 95.0
X Ray Diffraction 5.512 6.051 566 -- 566 0.19 -- -- 95.0
X Ray Diffraction 6.051 6.891 566 -- 566 0.182 -- -- 94.0
X Ray Diffraction 6.891 8.552 585 -- 585 0.154 -- -- 95.0
X Ray Diffraction 8.552 19.204 569 -- 569 0.17 -- -- 93.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic and tls
Mean Isotropic B 45.294
Anisotropic B[1][1] -0.401
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.404
Anisotropic B[2][2] 0.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.42
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.622
f_dihedral_angle_d 9.793
f_nbd_refined 4.063
f_plane_restr 0.002
f_chiral_restr 0.046
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4510
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 383

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection