X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 30% PEG 6000, 0.2M sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.34 α = 90
b = 59.87 β = 90
c = 66.28 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++ -- 2012-01-04
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 98.5 0.057 -- -- 3.3 17039 16782 -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)
1.76 1.82 95.7 0.366 -- -- 3.0 1610

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 1.753 30.264 -- 0.0 16745 16430 1641 96.13 0.2169 0.2169 0.2146 0.236 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 1.7534 1.805 -- 110 1021 0.3221 0.3175 -- 81.0
X Ray Diffraction 1.805 1.8632 -- 130 1181 0.2692 0.2708 -- 92.0
X Ray Diffraction 1.8632 1.9298 -- 133 1187 0.2428 0.2674 -- 95.0
X Ray Diffraction 1.9298 2.0071 -- 136 1206 0.2243 0.2567 -- 96.0
X Ray Diffraction 2.0071 2.0984 -- 136 1224 0.2148 0.2291 -- 97.0
X Ray Diffraction 2.0984 2.209 -- 137 1246 0.2259 0.2706 -- 97.0
X Ray Diffraction 2.209 2.3473 -- 138 1245 0.2219 0.2483 -- 98.0
X Ray Diffraction 2.3473 2.5285 -- 139 1250 0.2204 0.2221 -- 98.0
X Ray Diffraction 2.5285 2.7828 -- 142 1273 0.222 0.2474 -- 99.0
X Ray Diffraction 2.7828 3.1851 -- 143 1293 0.2264 0.2182 -- 99.0
X Ray Diffraction 3.1851 4.0114 -- 144 1290 0.1788 0.2049 -- 100.0
X Ray Diffraction 4.0114 30.2689 -- 153 1373 0.1981 0.2347 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.5903
Anisotropic B[1][1] 1.4752
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.0784
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.0728
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.754
f_plane_restr 0.005
f_chiral_restr 0.061
f_angle_d 0.877
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1177
Nucleic Acid Atoms 186
Heterogen Atoms 0
Solvent Atoms 192

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