X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details NANODROP, 20.0% Glycerol, 0.04M KH2PO4, 16.0% PEG 8000, no buffer, no pH, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details NANODROP, 0.2M MgCl2, 10.0% PEG 3000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.93 α = 90
b = 76.79 β = 90
c = 129.11 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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2007-08-19
Diffraction Radiation
Monochromator Protocol
Si(111) Double crystal MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-D 0.99187 APS 23-ID-D
SYNCHROTRON APS BEAMLINE 23-ID-D 0.97957, 0.95373 APS 23-ID-D

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
1.7 29.76 90.8 0.0667 -- -- 5.17 -- 73034 -- -3.0 33.512
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)
1.7 1.8 92.7 0.6278 -- 2.48 4.02 --

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 1.7 29.761 -- 0.0 -- 72956 3714 90.75 -- 0.183 0.181 0.221 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 1.7 1.744 -- 279 5113 0.254 0.313 -- 91.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.243
Anisotropic B[1][1] 0.95
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.68
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.27
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 2.199
r_chiral_restr 0.067
r_mcbond_it 1.5
r_gen_planes_refined 0.004
r_symmetry_vdw_refined 0.158
r_symmetry_vdw_other 0.191
r_dihedral_angle_3_deg 12.403
r_mcbond_other 0.335
r_bond_other_d 0.001
r_dihedral_angle_4_deg 16.17
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 3.671
r_nbd_other 0.17
r_nbtor_refined 0.174
r_angle_refined_deg 1.238
r_nbd_refined 0.224
r_nbtor_other 0.084
r_angle_other_deg 0.751
r_scangle_it 5.441
r_dihedral_angle_2_deg 27.9
r_xyhbond_nbd_refined 0.186
r_scbond_it 3.826
r_bond_refined_d 0.017
r_xyhbond_nbd_other 0.126
r_symmetry_hbond_refined 0.207
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5571
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 611

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0005
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.000
MAR345 data collection version: CCD
XDS data reduction
SHARP phasing