X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 298.0
Details 0.1 M Hepes (pH 7.5), 1 M succinic Acid, 1% (w/v) PEG MME 2000, temperature 298K, VAPOR DIFFUSION, HANGING DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 118.78 α = 90
b = 121.03 β = 90
c = 122.63 γ = 90
Symmetry
Space Group I 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2009
Diffraction Radiation
Monochromator Protocol
VARIMAX SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE -- 1.5418 -- --

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
2.32 50 99.7 0.097 -- -- 7.0 -- 38433 -- -- --
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)
2.32 2.36 97.5 0.498 -- -- 4.3 1855

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 2.32 28.71 -- 0.0 -- 38418 1958 99.7 -- 0.2134 0.2105 0.2659 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 2.32 2.38 -- 137 2580 0.275 0.426 -- 96.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.8034
Anisotropic B[1][1] 1.51
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.27
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.572
r_scbond_it 3.536
r_mcangle_it 2.085
r_mcbond_it 1.138
r_gen_planes_refined 0.01
r_chiral_restr 0.139
r_dihedral_angle_4_deg 13.356
r_dihedral_angle_3_deg 16.558
r_dihedral_angle_2_deg 33.602
r_dihedral_angle_1_deg 6.691
r_angle_refined_deg 1.952
r_bond_refined_d 0.023
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4033
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 294

Software

Computing
Computing Package Purpose
SCALEPACK Data Reduction (data scaling)
REFMAC 5.5.0072 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 version: 5.5.0072 refinement
SCALEPACK data reduction