X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details PROTEIN: 10 MG/ML in 0.01M HEPES pH 7.0, 0.3 M NaCl, 0.001 M DTT; RESERVOIR: 0.1M Hepes pH7.5, 0.2 M lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.76 α = 90
b = 113.15 β = 90
c = 210.68 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 MARMOSAIC 225 mm CCD -- 2009-08-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0000 APS 22-BM

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
2.7 50 99.9 0.1 -- -- 6.9 -- 29676 -- -- --
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)
2.7 2.8 100.0 0.636 -- -- 6.1 2866

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 2.7 44.058 -- 1.34 -- 29598 2000 99.5 -- 0.1796 0.1756 0.2361 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 2.6999 2.7674 -- 132 1821 0.2435 0.2957 -- 94.0
X Ray Diffraction 2.7674 2.8422 -- 140 1927 0.2411 0.3039 -- 100.0
X Ray Diffraction 2.8422 2.9258 -- 142 1963 0.2394 0.3327 -- 100.0
X Ray Diffraction 2.9258 3.0202 -- 137 1903 0.2343 0.2766 -- 100.0
X Ray Diffraction 3.0202 3.1281 -- 145 1988 0.2289 0.2932 -- 100.0
X Ray Diffraction 3.1281 3.2533 -- 139 1927 0.2129 0.312 -- 100.0
X Ray Diffraction 3.2533 3.4014 -- 144 1985 0.2083 0.2762 -- 100.0
X Ray Diffraction 3.4014 3.5806 -- 141 1949 0.1983 0.2264 -- 100.0
X Ray Diffraction 3.5806 3.8048 -- 143 1963 0.1753 0.2476 -- 100.0
X Ray Diffraction 3.8048 4.0984 -- 144 1975 0.1614 0.2335 -- 100.0
X Ray Diffraction 4.0984 4.5105 -- 144 2003 0.1379 0.2014 -- 100.0
X Ray Diffraction 4.5105 5.1623 -- 145 1999 0.1299 0.197 -- 100.0
X Ray Diffraction 5.1623 6.5006 -- 148 2044 0.1667 0.233 -- 100.0
X Ray Diffraction 6.5006 44.0639 -- 156 2151 0.1661 0.1963 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 67.2963
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.391
f_plane_restr 0.003
f_chiral_restr 0.049
f_angle_d 0.661
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6469
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 76

Software

Computing
Computing Package Purpose
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction