X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 8.5
Temperature 298.0
Details PEG 4000, Tris HCl, CuCl2, pH 8.5, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 56.75 α = 90
b = 74.67 β = 90
c = 114.92 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 DECTRIS PILATUS 6M -- 2011-12-03
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 -- 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
2.78 38.31 96.7 -- 0.099 -- 3.2 -- 12460 -- -3.0 --
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)
2.78 2.93 84.8 0.293 0.293 2.7 2.7 --

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 3.0 35.51 -- 1.35 12552 10076 504 98.27 -- 0.218 0.216 0.264 --
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 3.0004 3.3021 -- 123 2349 0.2575 0.2963 -- 99.0
X Ray Diffraction 3.3021 3.7795 -- 126 2386 0.2253 0.2969 -- 99.0
X Ray Diffraction 3.7795 4.7599 -- 125 2373 0.1823 0.2231 -- 98.0
X Ray Diffraction 4.7599 35.5114 -- 130 2464 0.2141 0.2595 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 32.8
Anisotropic B[1][1] -1.9498
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.6192
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.6694
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.063
f_dihedral_angle_d 13.404
f_angle_d 0.971
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3292
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 0

Software

Computing
Computing Package Purpose
XSCALE Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction