X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details 12-14% PEG 20000, 0.1M Mes or Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.14 α = 90
b = 110.14 β = 90
c = 80.17 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH Si mirrors 2005-06-10
CCD MARRESEARCH Si mirrors 2005-06-10
Diffraction Radiation
Monochromator Protocol
Si SINGLE WAVELENGTH
Si MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A 0.8793, 1.072, 1.071, 1.5218 EMBL/DESY, Hamburg BW7A
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8048 EMBL/DESY, Hamburg X13

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 55.06 98.5 0.058 -- -- 4.9 33892 33892 0.0 0.0 40.822
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 2.18 91.3 0.503 -- 2.6 3.6 3087

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
MAD 2.1 55.06 0.0 0.0 30976 30976 3087 93.6 0.239 0.239 0.232 0.292 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 2.11 614 62 552 0.395 0.387 -- --
X Ray Diffraction 2.11 2.13 619 69 550 0.34 0.312 -- --
X Ray Diffraction 2.13 2.14 597 60 537 0.323 0.418 -- --
X Ray Diffraction 2.14 2.16 599 63 536 0.323 0.356 -- --
X Ray Diffraction 2.16 2.18 534 51 483 0.297 0.354 -- --
X Ray Diffraction 2.18 2.19 518 50 468 0.302 0.336 -- --
X Ray Diffraction 2.19 2.21 518 45 473 0.322 0.351 -- --
X Ray Diffraction 2.21 2.23 598 47 551 0.293 0.318 -- --
X Ray Diffraction 2.23 2.24 649 57 592 0.39 0.386 -- --
X Ray Diffraction 2.24 2.26 632 63 569 0.308 0.346 -- --
X Ray Diffraction 2.26 2.28 522 46 476 0.317 0.337 -- --
X Ray Diffraction 2.28 2.3 485 44 441 0.349 0.454 -- --
X Ray Diffraction 2.3 2.32 515 50 465 0.34 0.455 -- --
X Ray Diffraction 2.32 2.34 596 63 533 0.325 0.386 -- --
X Ray Diffraction 2.34 2.37 536 53 483 0.287 0.335 -- --
X Ray Diffraction 2.37 2.39 598 66 532 0.297 0.356 -- --
X Ray Diffraction 2.39 2.41 586 55 531 0.266 0.345 -- --
X Ray Diffraction 2.41 2.44 621 67 554 0.275 0.372 -- --
X Ray Diffraction 2.44 2.46 598 60 538 0.263 0.337 -- --
X Ray Diffraction 2.46 2.49 619 57 562 0.255 0.309 -- --
X Ray Diffraction 2.49 2.52 612 54 558 0.238 0.3 -- --
X Ray Diffraction 2.52 2.55 582 51 531 0.265 0.35 -- --
X Ray Diffraction 2.55 2.58 648 79 569 0.262 0.338 -- --
X Ray Diffraction 2.58 2.61 619 66 553 0.235 0.299 -- --
X Ray Diffraction 2.61 2.65 617 78 539 0.269 0.301 -- --
X Ray Diffraction 2.65 2.68 634 64 570 0.243 0.34 -- --
X Ray Diffraction 2.68 2.72 624 54 570 0.247 0.352 -- --
X Ray Diffraction 2.72 2.76 629 57 572 0.277 0.33 -- --
X Ray Diffraction 2.76 2.8 622 50 572 0.263 0.349 -- --
X Ray Diffraction 2.8 2.85 641 61 580 0.244 0.332 -- --
X Ray Diffraction 2.85 2.9 646 74 572 0.235 0.308 -- --
X Ray Diffraction 2.9 2.95 626 72 554 0.244 0.341 -- --
X Ray Diffraction 2.95 3.01 638 68 570 0.24 0.31 -- --
X Ray Diffraction 3.01 3.07 649 52 597 0.257 0.286 -- --
X Ray Diffraction 3.07 3.14 649 68 581 0.243 0.281 -- --
X Ray Diffraction 3.14 3.21 634 57 577 0.253 0.349 -- --
X Ray Diffraction 3.21 3.29 672 84 588 0.257 0.342 -- --
X Ray Diffraction 3.29 3.38 641 57 584 0.253 0.3 -- --
X Ray Diffraction 3.38 3.48 666 68 598 0.258 0.282 -- --
X Ray Diffraction 3.48 3.59 656 86 570 0.254 0.311 -- --
X Ray Diffraction 3.59 3.72 661 62 599 0.237 0.276 -- --
X Ray Diffraction 3.72 3.87 668 80 588 0.226 0.291 -- --
X Ray Diffraction 3.87 4.04 660 59 601 0.203 0.237 -- --
X Ray Diffraction 4.04 4.26 675 70 605 0.197 0.271 -- --
X Ray Diffraction 4.26 4.52 663 58 605 0.16 0.194 -- --
X Ray Diffraction 4.52 4.87 669 65 604 0.16 0.196 -- --
X Ray Diffraction 4.87 5.36 670 68 602 0.179 0.214 -- --
X Ray Diffraction 5.36 6.14 695 59 636 0.223 0.32 -- --
X Ray Diffraction 6.14 7.74 683 68 615 0.19 0.284 -- --
X Ray Diffraction 7.74 500.01 673 70 603 0.177 0.253 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 54.97
Anisotropic B[1][1] 3.075
Anisotropic B[1][2] 1.755
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.075
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.151
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.34773
c_bond_d 0.008005
c_improper_angle_d 0.91265
c_dihedral_angle_d 22.244
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.3
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Luzzati Sigma A (R-Free Set) 0.33
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3216
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 201

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
SOLOMON phasing
CNS refinement
PDB_EXTRACT data extraction version: 1.701
MAR345 data collection