X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 293.0
Details 100 mM sodium acetate, pH 4.5, 3 M sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 209.66 α = 90
b = 209.66 β = 90
c = 127.41 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR DECTRIS PILATUS 6M -- 2010-09-30
Diffraction Radiation
Monochromator Protocol
channel-cut Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID29 0.9763 ESRF ID29

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
3.2 46.83 99.8 -- 0.143 -- 5.1 17855 17855 0.0 0.0 --
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)
3.196 3.37 98.8 0.807 0.807 1.0 4.9 2578

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 3.196 46.833 -- 1.35 17855 17852 911 99.72 -- 0.1782 0.1766 0.2079 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 3.196 3.3641 -- 141 2380 0.3169 0.3389 -- 99.0
X Ray Diffraction 3.3641 3.5749 -- 123 2379 0.2351 0.2701 -- 100.0
X Ray Diffraction 3.5749 3.8508 -- 140 2395 0.1781 0.2144 -- 100.0
X Ray Diffraction 3.8508 4.238 -- 135 2420 0.1492 0.1932 -- 100.0
X Ray Diffraction 4.238 4.8507 -- 124 2413 0.1231 0.1509 -- 100.0
X Ray Diffraction 4.8507 6.1093 -- 131 2443 0.1516 0.1698 -- 100.0
X Ray Diffraction 6.1093 46.8381 -- 117 2511 0.1929 0.227 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 83.5621
Anisotropic B[1][1] -15.9794
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -15.9794
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 31.9588
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.912
f_plane_restr 0.005
f_chiral_restr 0.087
f_angle_d 1.297
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2474
Nucleic Acid Atoms 0
Heterogen Atoms 15
Solvent Atoms 23

Software

Computing
Computing Package Purpose
DNA Data Collection
XDS Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7.2_869) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Phaser molecular replacement
SCALA version: 3.3.16 data reduction