X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 277.0
Details 30% PEG5000, 0.35M ammonium sulfate, 0.1M MES, pH 6.5, vapor diffusion, sitting drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 150.31 α = 90
b = 150.31 β = 90
c = 150.31 γ = 90
Symmetry
Space Group P 41 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 210 -- 2009-12-19
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1

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 53.15 99.5 0.089 0.089 -- 14.7 39431 39431 2.6 1.4 --
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)
2.0 2.11 99.4 0.55 0.55 1.4 7.0 --

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 2.0 53.141 -- 1.35 39360 39372 1999 99.16 -- 0.1736 0.1727 0.1912 --
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 2.0 2.0504 -- 158 2605 0.2335 0.259 -- 99.0
X Ray Diffraction 2.0504 2.1058 -- 145 2602 0.2106 0.2401 -- 99.0
X Ray Diffraction 2.1058 2.1678 -- 132 2646 0.2055 0.2463 -- 99.0
X Ray Diffraction 2.1678 2.2378 -- 162 2619 0.2074 0.2498 -- 100.0
X Ray Diffraction 2.2378 2.3177 -- 144 2632 0.1808 0.2271 -- 100.0
X Ray Diffraction 2.3177 2.4105 -- 137 2664 0.1766 0.2004 -- 100.0
X Ray Diffraction 2.4105 2.5202 -- 141 2656 0.1706 0.1653 -- 100.0
X Ray Diffraction 2.5202 2.6531 -- 154 2649 0.1682 0.167 -- 100.0
X Ray Diffraction 2.6531 2.8193 -- 138 2674 0.1668 0.1612 -- 100.0
X Ray Diffraction 2.8193 3.037 -- 135 2702 0.1688 0.1787 -- 100.0
X Ray Diffraction 3.037 3.3426 -- 125 2699 0.1694 0.1904 -- 100.0
X Ray Diffraction 3.3426 3.8261 -- 139 2707 0.1545 0.1812 -- 99.0
X Ray Diffraction 3.8261 4.82 -- 130 2726 0.1412 0.1534 -- 98.0
X Ray Diffraction 4.82 53.1599 -- 159 2792 0.1943 0.2115 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.219
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.046
f_dihedral_angle_d 12.873
f_angle_d 0.742
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2042
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 210

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA 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
REFMAC5 refinement
Phaser molecular replacement
SCALA version: 3.2.25 data reduction
Mosflm data collection