X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 290.0
Details 35% PEG 6000, 0.2M sodium formate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 40.87 α = 90
b = 59.24 β = 90
c = 65.76 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++ -- 2012-02-07
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
2.04 50 93.0 0.077 -- -- 2.4 10598 9855 -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)
2.05 2.12 95.0 0.411 -- -- 2.5 978

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 2.04 29.951 -- 0.0 9833 9514 951 89.38 0.2295 0.2295 0.226 0.2609 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 2.0397 2.1472 -- 121 1082 0.3077 0.3506 -- 81.0
X Ray Diffraction 2.1472 2.2817 -- 134 1207 0.2821 0.2967 -- 90.0
X Ray Diffraction 2.2817 2.4578 -- 136 1217 0.2492 0.3241 -- 91.0
X Ray Diffraction 2.4578 2.705 -- 136 1251 0.2584 0.3031 -- 93.0
X Ray Diffraction 2.705 3.0961 -- 140 1264 0.243 0.2999 -- 92.0
X Ray Diffraction 3.0961 3.8994 -- 139 1245 0.2024 0.2562 -- 90.0
X Ray Diffraction 3.8994 29.9545 -- 145 1297 0.2018 0.2109 -- 89.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.5819
Anisotropic B[1][1] 5.9957
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4473
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.2647
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 16.845
f_plane_restr 0.004
f_chiral_restr 0.076
f_angle_d 1.097
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1164
Nucleic Acid Atoms 184
Heterogen Atoms 0
Solvent Atoms 93

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