X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8
Temperature 298.0
Details PEG 8000, sodium chloride, TRIS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 108.31 α = 90
b = 131.63 β = 108.37
c = 159.16 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 ADSC QUANTUM 315 -- 2002-02-18
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.992 SSRL BL9-2

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
1.16 100 95.6 0.09 0.078 -- 2.5 1454519 1390520 1.0 1.0 12.34
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)
1.16 1.18 90.0 0.535 0.554 1.6 2.5 65290

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 1.16 50.0 0.0 0.0 1454519 1376724 13733 95.61 -- 0.12349 0.12323 0.14924 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 1.16 1.19 -- 953 96639 0.275 0.309 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.839
Anisotropic B[1][1] 0.26
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.13
Anisotropic B[2][2] -0.43
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.88
RMS Deviations
Key Refinement Restraint Deviation
r_xyhbond_nbd_other 0.382
r_scangle_it 5.698
r_sphericity_free 9.996
r_mcangle_it 2.894
r_symmetry_vdw_refined 0.396
r_angle_refined_deg 2.251
r_symmetry_vdw_other 0.373
r_dihedral_angle_1_deg 5.831
r_symmetry_hbond_refined 0.828
r_nbtor_other 1.049
r_dihedral_angle_3_deg 16.902
r_mcbond_it 2.258
r_chiral_restr 0.163
r_xyhbond_nbd_refined 0.225
r_rigid_bond_restr 2.613
r_bond_refined_d 0.029
r_gen_planes_refined 0.013
r_nbd_refined 0.333
r_scbond_it 4.054
r_sphericity_bonded 6.275
r_bond_other_d 0.001
r_angle_other_deg 1.039
r_nbd_other 0.263
r_gen_planes_other 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 32171
Nucleic Acid Atoms 0
Heterogen Atoms 192
Solvent Atoms 5021

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling