X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 20% PEG 3000, 0.2M sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.02 α = 90
b = 57.4 β = 90
c = 66.4 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR RIGAKU RAXIS IV++ -- 2011-12-09
Diffraction Radiation
Monochromator Protocol
osmic mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R 1.54 -- --

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
1.75 50 98.8 0.034 -- -- 3.0 17995 17770 -3.0 -3.0 --
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)
1.75 1.81 98.9 0.147 -- -- 2.9 1727

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 1.75 31.255 -- 0.0 17732 17626 1761 98.24 0.2246 0.2246 0.2214 0.2516 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 1.7497 1.797 -- 129 1166 0.3054 0.3102 -- 96.0
X Ray Diffraction 1.797 1.8498 -- 127 1184 0.2779 0.3252 -- 98.0
X Ray Diffraction 1.8498 1.9095 -- 134 1201 0.2472 0.2884 -- 98.0
X Ray Diffraction 1.9095 1.9778 -- 134 1194 0.2308 0.2784 -- 98.0
X Ray Diffraction 1.9778 2.0569 -- 135 1210 0.2278 0.2602 -- 99.0
X Ray Diffraction 2.0569 2.1505 -- 135 1206 0.2363 0.2873 -- 99.0
X Ray Diffraction 2.1505 2.2639 -- 133 1211 0.255 0.245 -- 99.0
X Ray Diffraction 2.2639 2.4057 -- 137 1231 0.2399 0.263 -- 99.0
X Ray Diffraction 2.4057 2.5913 -- 136 1226 0.2556 0.2322 -- 99.0
X Ray Diffraction 2.5913 2.852 -- 136 1220 0.2309 0.2786 -- 99.0
X Ray Diffraction 2.852 3.2643 -- 138 1243 0.2129 0.2307 -- 98.0
X Ray Diffraction 3.2643 4.1112 -- 140 1259 0.1885 0.2453 -- 98.0
X Ray Diffraction 4.1112 31.2597 -- 147 1314 0.2004 0.2273 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.979
Anisotropic B[1][1] 7.0316
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.0875
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.9441
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.539
f_plane_restr 0.003
f_chiral_restr 0.053
f_angle_d 0.813
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1169
Nucleic Acid Atoms 186
Heterogen Atoms 0
Solvent Atoms 172

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
HKL data reduction