X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 6
Temperature 291.0
Details 20% PEG 3350, 100 mM MES, 250 mM KCl, pH 6.0, VAPOR DIFFUSION, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.49 α = 90
b = 79.49 β = 90
c = 137.68 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2012-02-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04 0.9497 DIAMOND I04

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
2.6 39.7 100.0 0.156 0.156 -- 10.7 14021 14021 0.0 0.0 35.9
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)
2.6 2.66 99.9 0.599 -- -- 5.1 --

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
SAD 2.6 39.7 -- 0.0 14021 14021 1399 99.9 0.1975 0.1975 0.1928 0.24 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 2.606 2.6991 -- 134 1218 0.2119 0.3072 -- 97.0
X Ray Diffraction 2.6991 2.8072 -- 136 1218 0.2108 0.2688 -- 98.0
X Ray Diffraction 2.8072 2.9349 -- 136 1208 0.2112 0.3049 -- 99.0
X Ray Diffraction 2.9349 3.0896 -- 138 1242 0.2146 0.298 -- 99.0
X Ray Diffraction 3.0896 3.2831 -- 139 1259 0.2159 0.2737 -- 100.0
X Ray Diffraction 3.2831 3.5364 -- 139 1260 0.1928 0.2379 -- 100.0
X Ray Diffraction 3.5364 3.892 -- 138 1255 0.1813 0.2287 -- 100.0
X Ray Diffraction 3.892 4.4545 -- 141 1274 0.1625 0.2051 -- 100.0
X Ray Diffraction 4.4545 5.6097 -- 146 1306 0.1799 0.2177 -- 100.0
X Ray Diffraction 5.6097 39.7499 -- 152 1382 0.2044 0.2146 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.808
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.808
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.616
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.066
f_dihedral_angle_d 15.828
f_angle_d 1.063
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2186
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 52

Software

Computing
Computing Package Purpose
GDA Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7.3_928) Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHENIX version: (phenix.refine: 1.7.3_928) model building
GDA data collection