X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 10.5
Temperature 277.0
Details 30.0000% PEG-400, 0.1M CAPS pH 10.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.95 α = 90
b = 66.08 β = 90
c = 91 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 2008-10-11
Diffraction Radiation
Monochromator Protocol
Si(111) Double Crystal Monochrometer MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 0.94645,0.97967 APS 23-ID-B

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
1.59 29.04 99.0 0.044 -- -- 4.6 -- 37939 -- -3.0 20.169
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)
1.59 1.65 99.4 0.446 -- 1.7 -- --

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 1.59 29.037 -- 0.0 -- 37883 1890 99.69 -- 0.184 0.183 0.211 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 1.59 1.631 -- 133 2609 0.253 0.301 -- 99.85
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.121
Anisotropic B[1][1] 0.67
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.76
RMS Deviations
Key Refinement Restraint Deviation
r_nbtor_refined 0.172
r_gen_planes_other 0.001
r_angle_refined_deg 1.553
r_mcangle_it 2.62
r_angle_other_deg 0.949
r_dihedral_angle_3_deg 13.872
r_xyhbond_nbd_refined 0.147
r_nbd_refined 0.212
r_dihedral_angle_1_deg 5.683
r_nbd_other 0.208
r_nbtor_other 0.088
r_bond_refined_d 0.016
r_gen_planes_refined 0.006
r_symmetry_hbond_refined 0.155
r_mcbond_it 1.952
r_dihedral_angle_4_deg 15.995
r_chiral_restr 0.089
r_symmetry_vdw_refined 0.202
r_mcbond_other 0.47
r_bond_other_d 0.002
r_dihedral_angle_2_deg 36.782
r_symmetry_vdw_other 0.346
r_scbond_it 4.22
r_scangle_it 5.554
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2028
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 329

Software

Software
Software Name Purpose
REFMAC refinement version: 5.2.0019
PHENIX refinement
SHELX phasing
MolProbity model building version: 3beta29
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.006
XDS data reduction
SHELXD phasing
autoSHARP phasing