X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 291.0
Details 13% PEG 3350, 9% iso-propanol, 0.1M Tris pH 9.0, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 70.39 α = 90
b = 97.73 β = 110.89
c = 72.7 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 PSI PILATUS 6M -- 2012-07-16
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.075 NSLS X25

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
2.1 50 94.2 0.041 -- -- -- 50618 50618 0.0 -3.0 40.298
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)
2.1 2.16 64.1 0.32 -- 2.43 -- --

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 2.101 40.568 -- 1.99 50614 50614 2003 94.4 -- 0.1772 0.1755 0.2173 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 2.101 2.1537 -- 92 2364 0.2395 0.3294 -- 64.0
X Ray Diffraction 2.1537 2.2119 -- 118 2816 0.2111 0.271 -- 77.0
X Ray Diffraction 2.2119 2.277 -- 134 3215 0.2038 0.2915 -- 88.0
X Ray Diffraction 2.277 2.3505 -- 145 3525 0.1931 0.2505 -- 96.0
X Ray Diffraction 2.3505 2.4345 -- 154 3641 0.192 0.2875 -- 99.0
X Ray Diffraction 2.4345 2.5319 -- 146 3635 0.1882 0.2404 -- 100.0
X Ray Diffraction 2.5319 2.6471 -- 152 3655 0.1842 0.2559 -- 100.0
X Ray Diffraction 2.6471 2.7867 -- 152 3670 0.19 0.2234 -- 100.0
X Ray Diffraction 2.7867 2.9612 -- 146 3662 0.1889 0.2392 -- 100.0
X Ray Diffraction 2.9612 3.1898 -- 155 3677 0.184 0.2187 -- 100.0
X Ray Diffraction 3.1898 3.5106 -- 151 3653 0.1778 0.2306 -- 100.0
X Ray Diffraction 3.5106 4.0182 -- 150 3662 0.1595 0.1809 -- 100.0
X Ray Diffraction 4.0182 5.061 -- 149 3705 0.1481 0.1649 -- 100.0
X Ray Diffraction 5.061 40.568 -- 159 3731 0.1722 0.21 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.0837
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 11.476
f_plane_restr 0.003
f_chiral_restr 0.048
f_angle_d 0.723
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6580
Nucleic Acid Atoms 259
Heterogen Atoms 0
Solvent Atoms 367

Software

Computing
Computing Package Purpose
CBASS Data Collection
XDS Data Reduction (intensity integration)
XSCALE 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 molecular replacement
Xscale data reduction