X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 0.6 M trisodium citrate, 0.1 M sodium HEPES, pH 7.5, cryoprotectant: reservoir solution + 16% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.18 α = 90
b = 148.65 β = 90
c = 152.55 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2006-08
Diffraction Radiation
Monochromator Protocol
bent Ge(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 0.980 APS 14-BM-C

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
2.25 38.49 96.8 0.069 -- -- -- -- 107063 -- -3.0 37.478
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)
2.25 2.31 98.0 0.468 -- 3.88 -- --

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 2.25 38.49 -- 0.0 -- 106831 5471 96.61 -- 0.215 0.212 0.272 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 2.25 2.308 -- 797 7065 0.293 0.369 -- 97.75
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.54
Anisotropic B[1][1] -0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.07
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_other 0.199
r_angle_refined_deg 1.611
r_chiral_restr 0.094
r_bond_other_d 0.001
r_bond_refined_d 0.018
r_scbond_it 2.227
r_dihedral_angle_3_deg 14.71
r_gen_planes_refined 0.008
r_mcbond_it 0.798
r_mcangle_it 1.424
r_scangle_it 3.477
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 6.962
r_dihedral_angle_2_deg 36.679
r_dihedral_angle_4_deg 18.185
r_angle_other_deg 0.959
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15122
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 462

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
Phaser Structure Solution
REFMAC 5.5.0102 Structure Refinement
Software
Software Name Purpose
Xscale data reduction
REFMAC5 version: 5.5.0102 refinement
pdb_extract version: 3.10 data extraction