X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 295.0
Details 1.0 M sodium citrate, 0.1 M sodium cacodylate , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 139.58 α = 90
b = 39.16 β = 90
c = 53.58 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 200
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS HTC -- 2013-02-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178 -- --

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
1.75 28.8 100.0 -- 0.065 -- 6.4 -- 30556 -- -- 22.7
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)
1.75 1.84 100.0 -- 0.599 2.3 5.3 4401

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 1.75 28.8 -- 1.38 -- 30508 2000 99.94 -- 0.1727 0.1706 0.202 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 1.75 1.7938 -- 142 2023 0.2771 0.3445 -- 100.0
X Ray Diffraction 1.7938 1.8422 -- 139 1986 0.2358 0.2713 -- 100.0
X Ray Diffraction 1.8422 1.8964 -- 140 2004 0.209 0.2528 -- 100.0
X Ray Diffraction 1.8964 1.9576 -- 141 2006 0.21 0.2425 -- 100.0
X Ray Diffraction 1.9576 2.0276 -- 140 1992 0.193 0.2503 -- 100.0
X Ray Diffraction 2.0276 2.1088 -- 141 2005 0.1812 0.2335 -- 100.0
X Ray Diffraction 2.1088 2.2047 -- 143 2027 0.16 0.179 -- 100.0
X Ray Diffraction 2.2047 2.3209 -- 140 2018 0.1697 0.2012 -- 100.0
X Ray Diffraction 2.3209 2.4662 -- 143 2027 0.1741 0.2003 -- 100.0
X Ray Diffraction 2.4662 2.6565 -- 142 2025 0.1817 0.2274 -- 100.0
X Ray Diffraction 2.6565 2.9236 -- 143 2042 0.1784 0.2216 -- 100.0
X Ray Diffraction 2.9236 3.3461 -- 145 2068 0.1683 0.2137 -- 100.0
X Ray Diffraction 3.3461 4.2137 -- 147 2083 0.1431 0.1715 -- 100.0
X Ray Diffraction 4.2137 28.8 -- 154 2202 0.1525 0.159 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 26.5
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.123
f_plane_restr 0.004
f_bond_d 0.007
f_dihedral_angle_d 14.111
f_chiral_restr 0.072
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2087
Nucleic Acid Atoms 0
Heterogen Atoms 47
Solvent Atoms 253

Software

Software
Software Name Purpose
CrystalClear data collection
PHENIX refinement version: (phenix.refine: 1.8.2_1309)
XDS data reduction
XDS data scaling