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_scangle_it 3.477
r_scbond_it 2.227
r_mcangle_it 1.424
r_mcbond_other 0.199
r_bond_refined_d 0.018
r_bond_other_d 0.001
r_angle_refined_deg 1.611
r_angle_other_deg 0.959
r_dihedral_angle_1_deg 6.962
r_dihedral_angle_2_deg 36.679
r_dihedral_angle_3_deg 14.71
r_dihedral_angle_4_deg 18.185
r_chiral_restr 0.094
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_mcbond_it 0.798
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
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0102 refinement
Xscale data reduction