X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 81.19 α = 90
b = 102.19 β = 103.21
c = 99.53 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 -- -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL1-5 1.0 SSRL BL1-5

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
2.5 19.79 99.9 0.08 -- -- 3.7 54657 54657 0.0 0.0 55.1
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)
2.5 2.59 100.0 0.45 -- 2.5 3.69 5423

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 2.5 20.0 0.0 0.0 54121 54121 2767 98.87 0.227 0.227 0.225 0.254 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 2.5 2.586 -- 243 4891 0.323 0.365 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.082
Anisotropic B[1][1] 0.35
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.27
Anisotropic B[2][2] -0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.4
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 1.606
r_bond_refined_d 0.005
r_angle_refined_deg 0.86
r_dihedral_angle_1_deg 4.978
r_chiral_restr 0.054
r_gen_planes_refined 0.002
r_nbd_refined 0.161
r_xyhbond_nbd_refined 0.096
r_symmetry_vdw_refined 0.179
r_symmetry_hbond_refined 0.054
r_mcbond_it 1.066
r_mcangle_it 1.894
r_scbond_it 0.967
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8785
Nucleic Acid Atoms 0
Heterogen Atoms 123
Solvent Atoms 100

Software

Computing
Computing Package Purpose
D*TREK Data Reduction (data scaling)
REFMAC 5.1.19 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 1.700 data extraction
REFMAC5 version: 5.1.19 refinement
D*trek data processing