X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 290.0
Details 30 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.5, 25 % (w/v) PEG 1500

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.28 α = 90
b = 66.28 β = 90
c = 35.19 γ = 120
Symmetry
Space Group P 62

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-03-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1

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 30 100.0 -- -- -- 16.6 -- 9693 -- -- --
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 -- -- -- -- -- --

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 1.7 30.003 -- 1.66 -- 9677 976 98.28 -- 0.1992 0.1961 0.2276 --
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 1.7002 1.7898 -- 123 1111 0.2315 0.2823 -- 88.0
X Ray Diffraction 1.7898 1.9019 -- 137 1240 0.2008 0.2269 -- 100.0
X Ray Diffraction 1.9019 2.0487 -- 139 1257 0.1885 0.2517 -- 100.0
X Ray Diffraction 2.0487 2.2548 -- 143 1254 0.1811 0.2135 -- 100.0
X Ray Diffraction 2.2548 2.581 -- 142 1258 0.1894 0.2268 -- 100.0
X Ray Diffraction 2.581 3.2511 -- 145 1276 0.2096 0.2182 -- 100.0
X Ray Diffraction 3.2511 30.008 -- 147 1305 0.1923 0.2258 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_bond_d 0.007
f_chiral_restr 0.06
f_plane_restr 0.004
f_dihedral_angle_d 12.701
f_angle_d 1.071
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 582
Nucleic Acid Atoms 82
Heterogen Atoms 0
Solvent Atoms 53

Software

Software
Software Name Purpose
PHENIX refinement version: 1.9_1692
HKL-2000 data reduction
HKL-2000 data scaling
PHENIX phasing