X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 295.0
Details 1.2 M sodium/potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 204.15 α = 90
b = 216.21 β = 90
c = 420.98 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 325 mm CCD -- 2008-08-08
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2

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
3.8 210.49 98.6 0.093 0.093 -- 3.9 -- 89990 -- -- --
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)
3.8 4.01 99.3 0.545 0.545 1.3 3.9 13147

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 3.8 50.0 -- 0.0 -- 87509 4320 95.51 -- 0.268 0.263 0.313 RANDOM
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 188.144
Anisotropic B[1][1] 57.328
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -22.441
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -34.888
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.363
r_chiral_restr 0.09
r_scbond_it 22.238
r_gen_planes_refined 0.005
r_mcbond_it 36.389
r_dihedral_angle_1_deg 5.222
r_bond_refined_d 0.013
r_dihedral_angle_2_deg 42.006
r_dihedral_angle_3_deg 17.839
r_mcangle_it 49.942
r_dihedral_angle_4_deg 17.78
r_scangle_it 30.115
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 29020
Nucleic Acid Atoms 0
Heterogen Atoms 9
Solvent Atoms 0

Software

Software
Software Name Purpose
SCALA data scaling version: 3.2.25
PHASER phasing version: 2.1.4
REFMAC refinement version: 5.5.0088
PDB_EXTRACT data extraction version: 3.005
CNS refinement version: 1.2