X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 298.0
Details 2.4 M sodium malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.36 α = 90
b = 63.62 β = 90
c = 71.58 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
PIXEL PSI PILATUS 6M -- 2012-02-26
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen-cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 1.0000 SSRL BL12-2

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
2.4 29.07 98.2 0.133 -- -- 3.3 -- 9092 -- -- --
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)
2.4 2.46 98.7 0.613 -- 1.8 3.3 666

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 2.4 29.069 -- 2.03 -- 9084 907 98.15 -- 0.1809 0.1737 0.2453 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 2.4001 2.5504 -- 149 1340 0.2481 0.3505 -- 99.0
X Ray Diffraction 2.5504 2.7472 -- 149 1340 0.2374 0.2998 -- 98.0
X Ray Diffraction 2.7472 3.0234 -- 148 1337 0.2152 0.3053 -- 99.0
X Ray Diffraction 3.0234 3.4602 -- 151 1357 0.1704 0.3106 -- 99.0
X Ray Diffraction 3.4602 4.3572 -- 151 1372 0.1286 0.1797 -- 98.0
X Ray Diffraction 4.3572 29.071 -- 159 1431 0.1571 0.1929 -- 97.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.07
f_dihedral_angle_d 15.186
f_angle_d 1.103
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1803
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 104

Software

Computing
Computing Package Purpose
BLU-ICE Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8_1066) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8_1066) refinement
PHASER model building
BLU-ICE data collection