X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 30% w/V PEG 3350, 0.2M sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.96 α = 90
b = 59.2 β = 90
c = 66.09 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++ -- 2011-12-28
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
1.82 50 95.0 0.072 -- -- 3.3 14900 14145 -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)
1.83 1.9 83.8 0.321 -- -- 2.5 1233

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 1.822 30.01 -- 0.0 14900 13797 1373 92.31 0.207 0.207 0.2054 0.2182 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 1.8216 1.8867 -- 105 951 0.2913 0.3908 -- 71.0
X Ray Diffraction 1.8867 1.9622 -- 126 1165 0.237 0.2697 -- 89.0
X Ray Diffraction 1.9622 2.0515 -- 137 1220 0.2112 0.2255 -- 92.0
X Ray Diffraction 2.0515 2.1597 -- 134 1221 0.2158 0.2491 -- 93.0
X Ray Diffraction 2.1597 2.2949 -- 140 1250 0.2128 0.2345 -- 94.0
X Ray Diffraction 2.2949 2.472 -- 140 1247 0.2077 0.2386 -- 94.0
X Ray Diffraction 2.472 2.7207 -- 142 1296 0.2129 0.2473 -- 97.0
X Ray Diffraction 2.7207 3.114 -- 144 1306 0.2128 0.2464 -- 97.0
X Ray Diffraction 3.114 3.9219 -- 146 1334 0.1845 0.1691 -- 98.0
X Ray Diffraction 3.9219 30.014 -- 159 1434 0.195 0.1978 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.2916
Anisotropic B[1][1] -2.0054
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.9925
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.9871
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.844
f_plane_restr 0.003
f_chiral_restr 0.052
f_angle_d 0.797
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1169
Nucleic Acid Atoms 182
Heterogen Atoms 0
Solvent Atoms 196

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
DENZO data collection