X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details sodium/potassium phosphate buffer 1.9M, MPD 1%, glycerol (cryoprotection)

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.55 α = 90
b = 89.26 β = 110.67
c = 88.46 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
PIXEL DECTRIS PILATUS 2M-F -- 2012-03-17
Diffraction Radiation
Monochromator Protocol
Bartels SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 0.97780 SLS X06DA

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
2.8 44.63 98.0 -- 0.068 11.05 2.5 23165 23165 -- -- 55.17
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)
2.8 2.95 95.8 0.386 0.386 2.1 2.5 3301

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 2.8 44.629 -- 0.0 -- 23150 1158 97.79 -- 0.2588 0.2576 0.2809 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 2.799 2.872 -- 82 1544 0.344 0.407 -- 92.967
X Ray Diffraction 2.872 2.95 -- 83 1575 0.334 0.358 -- 98.398
X Ray Diffraction 2.95 3.035 -- 80 1528 0.301 0.319 -- 98.349
X Ray Diffraction 3.035 3.128 -- 79 1494 0.274 0.293 -- 98.006
X Ray Diffraction 3.128 3.23 -- 76 1447 0.278 0.316 -- 98.64
X Ray Diffraction 3.23 3.343 -- 74 1410 0.283 0.32 -- 98.933
X Ray Diffraction 3.343 3.468 -- 71 1353 0.27 0.286 -- 98.889
X Ray Diffraction 3.468 3.609 -- 70 1322 0.241 0.282 -- 98.584
X Ray Diffraction 3.609 3.769 -- 65 1239 0.243 0.319 -- 98.638
X Ray Diffraction 3.769 3.951 -- 63 1201 0.253 0.267 -- 98.137
X Ray Diffraction 3.951 4.163 -- 60 1136 0.243 0.348 -- 98.843
X Ray Diffraction 4.163 4.413 -- 59 1108 0.216 0.214 -- 99.15
X Ray Diffraction 4.413 4.715 -- 53 1017 0.206 0.22 -- 98.346
X Ray Diffraction 4.715 5.088 -- 49 926 0.221 0.211 -- 97.208
X Ray Diffraction 5.088 5.566 -- 46 871 0.241 0.254 -- 97.45
X Ray Diffraction 5.566 6.211 -- 41 773 0.275 0.274 -- 97.02
X Ray Diffraction 6.211 7.149 -- 37 705 0.291 0.299 -- 97.632
X Ray Diffraction 7.149 8.7 -- 31 600 0.237 0.208 -- 97.377
X Ray Diffraction 8.7 12.076 -- 24 472 0.238 0.221 -- 97.638
X Ray Diffraction 12.076 44.629 -- 15 270 0.336 0.46 -- 91.054
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.941
Anisotropic B[1][1] -2.91
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.39
Anisotropic B[2][2] 6.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.52
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.004
r_angle_other_deg 0.648
r_chiral_restr 0.051
r_dihedral_angle_1_deg 4.941
r_dihedral_angle_4_deg 16.203
r_bond_other_d 0.001
r_dihedral_angle_2_deg 30.311
r_angle_refined_deg 0.859
r_bond_refined_d 0.004
r_dihedral_angle_3_deg 11.81
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.20
XDS data scaling
PDB_EXTRACT data extraction version: 3.14
PHASER phasing
REFMAC refinement version: 5.7.0032