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 = 42.27 α = 90
b = 41.58 β = 104.53
c = 72.29 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 2011-06-03
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
1.6 50 90.7 -- 0.044 -- 3.2 29313 28593 1.0 2.0 24.3
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)
1.6 1.66 96.9 0.305 -- -- 3.1 3090

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 1.6 22.886 -- 0.0 29306 28593 1983 88.41 0.189 0.1816 0.1794 0.2113 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 1.5999 1.6399 -- 161 1901 0.3595 0.3889 -- 90.0
X Ray Diffraction 1.6399 1.6842 -- 135 1979 0.2902 0.3039 -- 92.0
X Ray Diffraction 1.6842 1.7338 -- 141 1954 0.2247 0.2229 -- 92.0
X Ray Diffraction 1.7338 1.7897 -- 145 1948 0.1912 0.2367 -- 92.0
X Ray Diffraction 1.7897 1.8536 -- 151 1955 0.1693 0.2226 -- 90.0
X Ray Diffraction 1.8536 1.9278 -- 118 1726 0.1786 0.2126 -- 81.0
X Ray Diffraction 1.9278 2.0155 -- 146 1904 0.167 0.2215 -- 89.0
X Ray Diffraction 2.0155 2.1217 -- 142 2010 0.178 0.2071 -- 93.0
X Ray Diffraction 2.1217 2.2545 -- 128 1648 0.1865 0.2263 -- 78.0
X Ray Diffraction 2.2545 2.4284 -- 154 2033 0.1714 0.2084 -- 95.0
X Ray Diffraction 2.4284 2.6725 -- 166 2149 0.1744 0.221 -- 100.0
X Ray Diffraction 2.6725 3.0584 -- 158 2156 0.1783 0.1892 -- 100.0
X Ray Diffraction 3.0584 3.8503 -- 95 1265 0.1633 0.2067 -- 96.0
X Ray Diffraction 3.8503 22.8879 -- 143 1982 0.1477 0.1638 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.0794
Anisotropic B[1][1] -0.7197
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.3403
Anisotropic B[2][2] 0.5698
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.1499
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.836
f_plane_restr 0.005
f_chiral_restr 0.077
f_angle_d 1.089
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2050
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 271

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
HKL-2000 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