X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details 0.2 M magnesium chloride, 0.1 M Bis-Tris pH 6.5, 25 %(w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.14 α = 90
b = 74.22 β = 90.11
c = 76.6 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 315r mirrors 2011-10-30
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID

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
1.35 50 96.5 -- 0.061 -- 7.2 162811 162811 0.0 0.0 14.23
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)
1.35 1.36 69.1 -- 0.582 2.0 4.0 5774

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
MIR 1.351 34.036 -- 0.0 162771 162771 8178 96.21 0.145 0.145 0.143 0.1805 random, 5%
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 1.351 1.3663 3526 170 3356 0.2968 0.3564 -- 63.0
X Ray Diffraction 1.3663 1.3824 4096 231 3865 0.2796 0.3079 -- 73.0
X Ray Diffraction 1.3824 1.3993 4488 249 4239 0.2492 0.3094 -- 80.0
X Ray Diffraction 1.3993 1.417 4837 287 4550 0.2232 0.2857 -- 86.0
X Ray Diffraction 1.417 1.4356 5113 231 4882 0.2095 0.2432 -- 91.0
X Ray Diffraction 1.4356 1.4553 5358 276 5082 0.1958 0.2717 -- 95.0
X Ray Diffraction 1.4553 1.4761 5532 298 5234 0.1826 0.2403 -- 98.0
X Ray Diffraction 1.4761 1.4981 5572 245 5327 0.1559 0.2196 -- 100.0
X Ray Diffraction 1.4981 1.5215 5620 273 5347 0.1399 0.2103 -- 100.0
X Ray Diffraction 1.5215 1.5465 5663 278 5385 0.1371 0.1788 -- 100.0
X Ray Diffraction 1.5465 1.5731 5621 265 5356 0.1324 0.2022 -- 100.0
X Ray Diffraction 1.5731 1.6017 5600 276 5324 0.1341 0.1809 -- 100.0
X Ray Diffraction 1.6017 1.6325 5640 257 5383 0.1171 0.2058 -- 100.0
X Ray Diffraction 1.6325 1.6659 5662 277 5385 0.1103 0.1669 -- 100.0
X Ray Diffraction 1.6659 1.7021 5572 272 5300 0.108 0.164 -- 100.0
X Ray Diffraction 1.7021 1.7417 5667 283 5384 0.11 0.1668 -- 100.0
X Ray Diffraction 1.7417 1.7852 5601 253 5348 0.1181 0.1666 -- 100.0
X Ray Diffraction 1.7852 1.8335 5623 281 5342 0.1243 0.1691 -- 100.0
X Ray Diffraction 1.8335 1.8874 5619 296 5323 0.1225 0.1907 -- 100.0
X Ray Diffraction 1.8874 1.9484 5668 277 5391 0.1246 0.1736 -- 100.0
X Ray Diffraction 1.9484 2.018 5651 283 5368 0.1303 0.1624 -- 100.0
X Ray Diffraction 2.018 2.0988 5623 260 5363 0.1355 0.1746 -- 100.0
X Ray Diffraction 2.0988 2.1943 5653 292 5361 0.1362 0.1771 -- 100.0
X Ray Diffraction 2.1943 2.3099 5677 301 5376 0.1329 0.1575 -- 100.0
X Ray Diffraction 2.3099 2.4546 5628 256 5372 0.1394 0.1702 -- 100.0
X Ray Diffraction 2.4546 2.6441 5683 307 5376 0.1381 0.176 -- 100.0
X Ray Diffraction 2.6441 2.91 5642 305 5337 0.1467 0.1673 -- 100.0
X Ray Diffraction 2.91 3.3308 5696 315 5381 0.1511 0.1934 -- 100.0
X Ray Diffraction 3.3308 4.1953 5677 306 5371 0.1386 0.1519 -- 100.0
X Ray Diffraction 4.1953 34.0464 5763 278 5485 0.1583 0.1805 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
Mean Isotropic B 19.9
Anisotropic B[1][1] -0.1296
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.4325
Anisotropic B[2][2] -1.3972
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.5268
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.08
f_dihedral_angle_d 12.562
f_angle_d 1.147
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6937
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 1049

Software

Computing
Computing Package Purpose
sBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000, Molrep Structure Solution
PHENIX (phenix.refine: 1.7.3_920) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_920) refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
sBCCOLLECT data collection