X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Temperature 293.0
Details 20% PEG 3350, 0.2M K Formate, no buffer, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 135.71 α = 90
b = 68.36 β = 93.69
c = 107.83 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2011-11-14
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT -- -- --

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
2.4 50 99.5 0.098 -- -- -- -- 75296 -- 2.0 25.25
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)
2.4 2.46 99.6 0.371 -- 4.88 -- --

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 2.4 43.51 -- 2.0 38729 38729 1947 99.8 -- 0.205 0.202 0.256 --
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 2.4002 2.4602 -- 168 2630 0.2504 0.3251 -- 100.0
X Ray Diffraction 2.4602 2.5267 -- 128 2601 0.2102 0.2643 -- 100.0
X Ray Diffraction 2.5267 2.6011 -- 122 2623 0.2243 0.2968 -- 100.0
X Ray Diffraction 2.6011 2.685 -- 138 2577 0.2107 0.2957 -- 100.0
X Ray Diffraction 2.685 2.781 -- 124 2656 0.2124 0.2825 -- 100.0
X Ray Diffraction 2.781 2.8923 -- 126 2609 0.1881 0.2715 -- 100.0
X Ray Diffraction 2.8923 3.0239 -- 142 2598 0.2192 0.29 -- 98.0
X Ray Diffraction 3.0239 3.1833 -- 136 2595 0.1996 0.2766 -- 99.0
X Ray Diffraction 3.1833 3.3826 -- 137 2624 0.1916 0.2293 -- 100.0
X Ray Diffraction 3.3826 3.6437 -- 158 2626 0.19 0.2165 -- 100.0
X Ray Diffraction 3.6437 4.0101 -- 138 2651 0.1849 0.2482 -- 100.0
X Ray Diffraction 4.0101 4.5899 -- 120 2646 0.1512 0.1666 -- 100.0
X Ray Diffraction 4.5899 5.7806 -- 161 2634 0.1878 0.2311 -- 100.0
X Ray Diffraction 5.7806 43.5169 -- 149 2712 0.2786 0.3308 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.96
Anisotropic B[1][1] -1.6516
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.8773
Anisotropic B[2][2] -2.7902
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.4418
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.071
f_dihedral_angle_d 12.426
f_angle_d 1.081
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5654
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 488

Software

Computing
Computing Package Purpose
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (PHENIX.REFINE: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
mlphare phasing
Xscale data reduction