X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.8
Temperature 277.0
Details 32% PEG400, 0.1 M HEPES, pH 7.8, vapor diffusion, sitting drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.88 α = 90
b = 115.04 β = 90
c = 125.57 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 ADSC QUANTUM 315r -- 2009-05-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 0.97971 SSRL BL7-1

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
1.9 50 100.0 0.093 -- -- 7.1 -- 131348 -- -- --
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)
1.9 1.97 99.9 0.611 -- -- 6.6 --

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 1.9 39.79 -- -- -- 131243 6603 99.8 -- 0.173 0.171 0.2 --
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 1.9 1.95 -- 462 8914 0.251 0.288 -- 97.29
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.16
Anisotropic B[1][1] -0.07
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.969
r_nbd_refined 0.198
r_xyhbond_nbd_refined 0.178
r_mcbond_it 3.538
r_angle_refined_deg 0.91
r_nbtor_refined 0.319
r_symmetry_hbond_refined 0.196
r_scbond_it 4.426
r_bond_refined_d 0.004
r_symmetry_vdw_refined 0.195
r_chiral_restr 0.061
r_dihedral_angle_1_deg 4.666
r_dihedral_angle_2_deg 32.223
r_dihedral_angle_4_deg 13.74
r_gen_planes_refined 0.002
r_dihedral_angle_3_deg 10.788
r_mcangle_it 3.938
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7034
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 1187

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MOLREP phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.005
HKL-2000 data collection