X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 8.2
Temperature 294.0
Details 50 mM HEPES pH 8.2, 50 mM MgCl2, 22% PEG4000, hanging drop, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.9 α = 90
b = 72.9 β = 90
c = 113.97 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD mirrors 2012-08-20
Diffraction Radiation
Monochromator Protocol
Si(111) 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
1.75 50 99.8 0.088 -- -- 8.3 31994 31923 1.0 1.0 29.0
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)
1.746 1.81 100.0 0.822 -- -- 7.2 3125

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 1.746 23.054 -- 1.38 31878 31868 2000 99.88 0.217 0.1723 0.1701 0.2045 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 1.746 1.7896 -- 138 2070 0.305 0.3455 -- 100.0
X Ray Diffraction 1.7896 1.838 -- 141 2087 0.268 0.3011 -- 100.0
X Ray Diffraction 1.838 1.892 -- 140 2097 0.2489 0.253 -- 100.0
X Ray Diffraction 1.892 1.9531 -- 140 2088 0.2226 0.2224 -- 100.0
X Ray Diffraction 1.9531 2.0228 -- 141 2120 0.1938 0.2131 -- 100.0
X Ray Diffraction 2.0228 2.1038 -- 141 2100 0.1793 0.2297 -- 100.0
X Ray Diffraction 2.1038 2.1995 -- 141 2104 0.1639 0.2313 -- 100.0
X Ray Diffraction 2.1995 2.3153 -- 141 2110 0.1675 0.2273 -- 100.0
X Ray Diffraction 2.3153 2.4602 -- 143 2134 0.163 0.2033 -- 100.0
X Ray Diffraction 2.4602 2.6499 -- 144 2138 0.157 0.2243 -- 100.0
X Ray Diffraction 2.6499 2.9161 -- 144 2150 0.1701 0.1971 -- 100.0
X Ray Diffraction 2.9161 3.337 -- 144 2155 0.1502 0.1811 -- 100.0
X Ray Diffraction 3.337 4.2001 -- 146 2191 0.1431 0.1788 -- 100.0
X Ray Diffraction 4.2001 23.0563 -- 156 2324 0.1575 0.1778 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 25.9969
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.399
f_plane_restr 0.006
f_dihedral_angle_d 14.575
f_bond_d 0.011
f_chiral_restr 0.081
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1795
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 303

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing version: 2.5.0
PHENIX refinement version: 1.8.2_1309
PDB_EXTRACT data extraction version: 3.11
SERGUI data collection