X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop Nanodrop
pH 8.5
Temperature 277.0
Details 0.2M MgCl2, 30.0% PEG-4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.75 α = 90
b = 71.59 β = 90
c = 83.2 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2006-06-05
Diffraction Radiation
Monochromator Protocol
Double crystal monochromator MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837, 0.97915, 0.97929 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
1.8 27.95 92.2 0.069 -- -- -- -- 21098 -- -- 25.562
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)
1.8 1.86 72.7 0.477 -- 1.6 -- 2718

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
MAD 1.8 27.951 -- 0.0 -- 21060 1084 97.65 -- 0.192 0.189 0.247 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 1.8 1.847 1258 57 1201 0.297 0.358 -- 82.28
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.764
Anisotropic B[1][1] 2.23
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.7
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 7.139
r_scangle_it 3.195
r_symmetry_hbond_refined 0.171
r_chiral_restr 0.076
r_mcangle_it 1.268
r_xyhbond_nbd_refined 0.163
r_metal_ion_refined 0.046
r_dihedral_angle_2_deg 34.064
r_angle_other_deg 0.8
r_nbtor_refined 0.176
r_mcbond_other 0.21
r_angle_refined_deg 1.366
r_gen_planes_refined 0.006
r_bond_other_d 0.001
r_mcbond_it 0.955
r_symmetry_vdw_refined 0.08
r_dihedral_angle_4_deg 18.147
r_nbd_other 0.181
r_bond_refined_d 0.015
r_gen_planes_other 0.001
r_nbtor_other 0.084
r_dihedral_angle_3_deg 11.989
r_nbd_refined 0.211
r_symmetry_vdw_other 0.244
r_scbond_it 2.231
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1744
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 235

Software

Software
Software Name Purpose
MolProbity model building version: 3beta29
REFMAC refinement version: 5.2.0005
XSCALE data scaling
PDB_EXTRACT data extraction version: 2.000
XDS data reduction