X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.6
Temperature 293.0
Details PEG 5000 MME 17%, 0.15 M KSCN, 0.1 M Tris(HOAc) pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.65 α = 90
b = 126.99 β = 90
c = 136.78 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 DYNAMICALLY BENDABLE MIRROR 2008-06-25
Diffraction Radiation
Monochromator Protocol
LN2 COOLED FIXED EXIT SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0000 SLS X06SA

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
2.05 30 98.9 -- 0.079 -- 6.7 -- 63157 -- -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)
2.05 2.2 95.0 -- 0.431 4.5 -- --

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 2.051 29.41 -- 1.36 -- 63122 875 99.04 -- 0.1816 0.1811 0.218 --
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 2.051 2.1795 -- 137 9819 0.2113 0.2506 -- 95.0
X Ray Diffraction 2.1795 2.3477 -- 143 10305 0.1867 0.2635 -- 100.0
X Ray Diffraction 2.3477 2.5839 -- 147 10393 0.1817 0.2267 -- 100.0
X Ray Diffraction 2.5839 2.9575 -- 148 10418 0.1827 0.212 -- 100.0
X Ray Diffraction 2.9575 3.7249 -- 148 10487 0.1776 0.2297 -- 100.0
X Ray Diffraction 3.7249 29.4135 -- 152 10825 0.1711 0.1899 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Anisotropic B[1][1] -2.4474
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.3455
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.1019
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.073
f_bond_d 0.007
f_angle_d 1.088
f_plane_restr 0.012
f_dihedral_angle_d 16.59
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6838
Nucleic Acid Atoms 0
Heterogen Atoms 25
Solvent Atoms 577

Software

Software
Software Name Purpose
XSCALE data processing
PHENIX refinement version: 1.5_2
PDB_EXTRACT data extraction version: 3.100
XDS data reduction
XSCALE data scaling
PHASER phasing