X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 291.0
Details 1.2 M sodium citrate, 5% MPD, 0.1 M sodium HEPES, 3 molar equivalents of H3K4me3 peptide., pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.17 α = 90
b = 87.07 β = 95.65
c = 76.57 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2011-04-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.28292 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
2.65 37.8 98.7 0.073 -- -- -- -- 20804 -- -3.0 67.802
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)
2.65 2.72 98.3 0.946 -- 1.94 -- --

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
SAD 2.65 37.8 -- 0.0 -- 20787 985 98.76 -- 0.2102 0.2085 0.2416 THIN SHELLS (SFTOOLS)
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 2.65 2.79 -- 147 2850 0.2299 0.2388 -- 98.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 66.9971
Anisotropic B[1][1] 9.6709
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.6329
Anisotropic B[2][2] -12.7657
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.0948
RMS Deviations
Key Refinement Restraint Deviation
t_other_torsion 18.52
t_omega_torsion 2.65
t_angle_deg 1.01
t_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.347
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3947
Nucleic Acid Atoms 0
Heterogen Atoms 23
Solvent Atoms 0

Software

Computing
Computing Package Purpose
xds Data Reduction (intensity integration)
xscale Data Reduction (data scaling)
shelx Structure Solution
BUSTER 2.10.0 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
BUSTER-TNT version: BUSTER 2.10.0 refinement
SHARP density modification
SHELX phasing
Xscale data reduction