X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 298.0
Details 20% PEG 3350 200 mM CaCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 88.08 α = 90
b = 88.08 β = 90
c = 133.9 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM

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
1.73 50 100.0 0.1 -- -- 10.8 21088 21088 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)
1.73 1.76 100.0 0.737 -- -- 8.5 1025

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 1.731 26.481 -- 1.35 21073 21073 1996 99.92 0.1721 0.1721 0.1694 0.1976 --
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 1.7307 1.774 -- 141 1346 0.2877 0.315 -- 100.0
X Ray Diffraction 1.774 1.822 -- 139 1335 0.2504 0.2797 -- 100.0
X Ray Diffraction 1.822 1.8756 -- 142 1350 0.2098 0.2605 -- 100.0
X Ray Diffraction 1.8756 1.9361 -- 138 1338 0.2133 0.2659 -- 100.0
X Ray Diffraction 1.9361 2.0053 -- 142 1357 0.1763 0.2025 -- 100.0
X Ray Diffraction 2.0053 2.0855 -- 142 1345 0.16 0.2211 -- 100.0
X Ray Diffraction 2.0855 2.1804 -- 142 1364 0.1596 0.1716 -- 100.0
X Ray Diffraction 2.1804 2.2953 -- 139 1335 0.1718 0.2213 -- 100.0
X Ray Diffraction 2.2953 2.439 -- 143 1359 0.175 0.2124 -- 100.0
X Ray Diffraction 2.439 2.6272 -- 144 1380 0.1554 0.1972 -- 100.0
X Ray Diffraction 2.6272 2.8912 -- 142 1350 0.1563 0.2084 -- 100.0
X Ray Diffraction 2.8912 3.3089 -- 144 1382 0.1618 0.1726 -- 100.0
X Ray Diffraction 3.3089 4.1663 -- 146 1389 0.1452 0.1551 -- 100.0
X Ray Diffraction 4.1663 26.4844 -- 152 1447 0.1695 0.1867 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.6507
Anisotropic B[1][1] 0.6438
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.6438
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.2876
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.071
f_plane_restr 0.004
f_bond_d 0.007
f_angle_d 1.173
f_dihedral_angle_d 20.07
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1309
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 169

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHENIX refinement version: 1.7.1_743
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
PHENIX phasing