X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 0.2 M sodium iodide, 20% w/v PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.79 α = 90
b = 69.89 β = 90
c = 79.21 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 315 -- 2012-12-07
Diffraction Radiation
Monochromator Protocol
Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E

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
1.5 25 99.9 0.082 -- -- 4.7 -- 60026 -- -- 13.5
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)
1.5 1.55 100.0 0.531 -- -- 4.7 5947

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 1.5 24.554 -- 1.36 -- 59959 1998 99.9 -- 0.1648 0.1644 0.1776 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 1.5001 1.5376 -- 135 4082 0.2332 0.2945 -- 99.0
X Ray Diffraction 1.5376 1.5792 -- 142 4084 0.207 0.2085 -- 100.0
X Ray Diffraction 1.5792 1.6257 -- 144 4110 0.1922 0.2384 -- 100.0
X Ray Diffraction 1.6257 1.6781 -- 143 4073 0.1845 0.2162 -- 100.0
X Ray Diffraction 1.6781 1.7381 -- 143 4094 0.1794 0.2003 -- 100.0
X Ray Diffraction 1.7381 1.8077 -- 142 4105 0.1649 0.1738 -- 100.0
X Ray Diffraction 1.8077 1.8899 -- 138 4141 0.1667 0.1807 -- 100.0
X Ray Diffraction 1.8899 1.9895 -- 144 4103 0.1565 0.1711 -- 100.0
X Ray Diffraction 1.9895 2.1141 -- 135 4120 0.1546 0.1986 -- 100.0
X Ray Diffraction 2.1141 2.2772 -- 144 4130 0.1579 0.172 -- 100.0
X Ray Diffraction 2.2772 2.5062 -- 142 4162 0.1652 0.1785 -- 100.0
X Ray Diffraction 2.5062 2.8683 -- 144 4178 0.1669 0.1624 -- 100.0
X Ray Diffraction 2.8683 3.612 -- 148 4195 0.1586 0.147 -- 100.0
X Ray Diffraction 3.612 24.5575 -- 154 4384 0.1517 0.1729 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.2771
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.722
f_plane_restr 0.005
f_chiral_restr 0.071
f_angle_d 1.088
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1796
Nucleic Acid Atoms 184
Heterogen Atoms 7
Solvent Atoms 354

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser version: 2.3.0 molecular replacement
HKL data reduction