X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7
Temperature 293.0
Details 16% PEG6000, 0.01M sodium citrate , pH 7.0, Vapor Diffusion, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 195.72 α = 90
b = 37.42 β = 94.66
c = 40.28 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Radiation
Monochromator Protocol
-- Single Wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
Synchrotron ESRF BEAMLINE ID29 1.0000 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
2.5 48.77 99.8 -- -- -- -- 10306 10306 3.2 3.2 31.68
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)
2.5 2.64 100.0 0.446 -- 3.2 4.1 1472

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 2.5 40.147 3.2 1.35 10302 10302 487 99.7 -- 0.2121 0.2101 0.252 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 2.5 2.8618 -- 164 3220 0.2701 0.3484 -- 100.0
X Ray Diffraction 2.8618 3.6052 -- 154 3251 0.2118 0.2711 -- 100.0
X Ray Diffraction 3.6052 40.152 -- 169 3344 0.1887 0.2107 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.3352
Anisotropic B[1][1] -6.4455
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.6395
Anisotropic B[2][2] 11.0554
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.6099
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.422
f_plane_restr 0.006
f_chiral_restr 0.08
f_angle_d 1.046
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1861
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 41

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
phenix Structure Solution
PHENIX (phenix.refine: dev_723) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement