X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.8
Temperature 293.0
Details 26% PEG 300, 0.1 M sodium acetate, 2% DMSO, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.65 α = 90
b = 119.71 β = 90
c = 164.83 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2011-07-14
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1 APS 21-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
1.64 96.9 88.6 -- -- -- -- 73747 65340 -- -- --
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)
1.64 1.7 94.8 0.2 -- 4.4 -- --

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 1.64 33.34 -- 0.0 73747 65335 3306 88.57 0.1895 0.1895 0.189 0.1985 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 1.64 1.682 -- 228 4592 0.282 0.288 -- 93.56
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.4155
Anisotropic B[1][1] 3.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.42
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.75
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_chiral_restr 0.085
r_dihedral_angle_4_deg 14.802
r_dihedral_angle_3_deg 11.61
r_dihedral_angle_2_deg 33.968
r_dihedral_angle_1_deg 5.102
r_angle_refined_deg 1.118
r_bond_refined_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2455
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 424

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.3.0 molecular replacement