X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 16% PEG 3350, 0.1M CaCl2, 0.1M Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 222.97 α = 90
b = 222.97 β = 90
c = 86.48 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR scanner 300 mm plate -- 2008-11-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1 APS 22-ID

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
2.77 48.27 63.3 0.13 0.088 -- 4.8 63180 39993 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)
2.75 2.85 12.0 0.456 0.61 1.2 1.9 --

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 3.4 48.27 -- 0.0 62593 31870 1520 93.64 -- 0.2805 0.2796 0.313 --
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 3.4004 3.5098 -- 93 2028 0.3313 0.3804 -- 66.0
X Ray Diffraction 3.5098 3.6349 -- 83 2344 0.3219 0.3387 -- 76.0
X Ray Diffraction 3.6349 3.78 -- 132 2554 0.2975 0.333 -- 84.0
X Ray Diffraction 3.78 3.9515 -- 144 2761 0.2858 0.3227 -- 90.0
X Ray Diffraction 3.9515 4.159 -- 164 2866 0.2748 0.3276 -- 94.0
X Ray Diffraction 4.159 4.4183 -- 133 2933 0.2486 0.2515 -- 95.0
X Ray Diffraction 4.4183 4.7574 -- 158 2926 0.2427 0.2491 -- 95.0
X Ray Diffraction 4.7574 5.2325 -- 178 2899 0.2509 0.2948 -- 94.0
X Ray Diffraction 5.2325 5.9812 -- 135 2958 0.281 0.3013 -- 96.0
X Ray Diffraction 5.9812 7.504 -- 128 2984 0.3062 0.3912 -- 96.0
X Ray Diffraction 7.504 25.5771 -- 172 3014 0.2747 0.3204 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -17.8341
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -17.8341
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -17.8485
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.002
f_chiral_restr 0.04
f_dihedral_angle_d 12.585
f_angle_d 0.916
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10548
Nucleic Acid Atoms 0
Heterogen Atoms 350
Solvent Atoms 93

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
phaser Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement