X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details 1.4 M Sodium Citrate 50 mM Tris pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.25 α = 90
b = 41.59 β = 104.44
c = 72.26 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2011-06-06
Diffraction Radiation
Monochromator Protocol
rigaku varimax HR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 1.5418 -- --

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
1.7 50 96.7 -- 0.037 -- 3.3 25852 25901 1.0 2.0 --
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)
1.7 1.76 98.1 0.094 -- -- 3.2 2618

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 1.699 23.819 -- 0.0 26105 25901 1984 95.81 0.17 0.174 0.1594 0.1914 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 1.6992 1.7417 -- 142 1657 0.2084 0.248 -- 94.0
X Ray Diffraction 1.7417 1.7887 -- 137 1665 0.1887 0.2578 -- 96.0
X Ray Diffraction 1.7887 1.8414 -- 143 1700 0.1651 0.2056 -- 96.0
X Ray Diffraction 1.8414 1.9008 -- 144 1675 0.1533 0.1884 -- 94.0
X Ray Diffraction 1.9008 1.9687 -- 136 1678 0.1487 0.1842 -- 95.0
X Ray Diffraction 1.9687 2.0475 -- 141 1704 0.1497 0.1785 -- 96.0
X Ray Diffraction 2.0475 2.1406 -- 151 1718 0.152 0.1818 -- 97.0
X Ray Diffraction 2.1406 2.2534 -- 139 1742 0.1554 0.209 -- 98.0
X Ray Diffraction 2.2534 2.3944 -- 143 1751 0.1608 0.2085 -- 98.0
X Ray Diffraction 2.3944 2.5791 -- 146 1786 0.1725 0.2037 -- 100.0
X Ray Diffraction 2.5791 2.8382 -- 152 1783 0.1715 0.2019 -- 100.0
X Ray Diffraction 2.8382 3.2481 -- 147 1790 0.1666 0.2115 -- 100.0
X Ray Diffraction 3.2481 4.0889 -- 115 1403 0.1434 0.1634 -- 78.0
X Ray Diffraction 4.0889 23.8217 -- 153 1860 0.1506 0.1601 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.4338
Anisotropic B[1][1] -1.1389
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.0705
Anisotropic B[2][2] 1.8739
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.735
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.319
f_plane_restr 0.005
f_chiral_restr 0.079
f_angle_d 1.095
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2047
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 280

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
HKL data reduction