X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 3.0 M sodium formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 210.95 α = 90
b = 210.95 β = 90
c = 323 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Toroidal Mirror 2009-07-27
Diffraction Radiation
Monochromator Protocol
Silicon (1 1 1) channel-cut SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-1 0.97625 ESRF ID23-1

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
2.56 100.5 98.0 0.115 -- -- 1.9 259578 259578 -- 2.0 42.386
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)
2.56 2.7 98.5 0.362 -- 1.7 1.9 37996

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 2.56 79.51 2.0 -- 246309 246309 13045 97.48 0.18867 0.18867 0.186 0.23895 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 2.56 2.626 18209 966 18209 0.291 0.351 -- 98.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.184
Anisotropic B[1][1] -0.03
Anisotropic B[1][2] -0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.05
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.692
r_dihedral_angle_4_deg 20.963
r_dihedral_angle_2_deg 39.446
r_scangle_it 4.655
r_dihedral_angle_1_deg 5.745
r_dihedral_angle_3_deg 20.266
r_mcbond_it 0.697
r_bond_refined_d 0.017
r_chiral_restr 0.116
r_gen_planes_refined 0.007
r_mcangle_it 1.468
r_scbond_it 2.689
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 34042
Nucleic Acid Atoms 0
Heterogen Atoms 268
Solvent Atoms 1525

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.5.0109
MOSFLM data reduction
SCALA data scaling