X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 277.0
Details 2-Methyl-2,4-Pentanediol (MPD), Tris-phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.6 α = 90
b = 74.94 β = 90
c = 50.99 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 116.1
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Mirrors 2002-01-26
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
1.64 100 97.2 0.053 -- -- 13.202 -- 50987 2.0 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)
1.64 1.67 77.9 0.353 -- 3.165 3.816 1946

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 1.64 50.0 0.0 0.0 50987 49436 2471 97.4 -- -- 0.1839 0.2084 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 1.64 1.7 3966 205 -- 0.3924 0.3862 -- 8.022
X Ray Diffraction 1.7 1.77 4642 213 -- 0.2882 0.3161 -- 9.389
X Ray Diffraction 1.77 1.85 4684 231 -- 0.2149 0.2219 -- 9.474
X Ray Diffraction 1.85 1.94 4697 232 -- 0.1842 0.2094 -- 9.5
X Ray Diffraction 1.94 2.07 4683 277 -- 0.1838 0.2053 -- 9.47
X Ray Diffraction 2.07 2.23 4746 245 -- 0.1801 0.2165 -- 9.6
X Ray Diffraction 2.23 2.45 4780 263 -- 0.1793 0.2009 -- 9.669
X Ray Diffraction 2.45 2.8 4820 256 -- 0.1764 0.2103 -- 9.74
X Ray Diffraction 2.8 3.53 4885 263 -- 0.1679 0.1983 -- 9.88
X Ray Diffraction 3.53 50.0 5062 286 -- 0.1657 0.1861 -- 10.23
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 21.0081
RMS Deviations
Key Refinement Restraint Deviation
o_bond_d 0.0051
c_angle_d 2.174
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2376
Nucleic Acid Atoms 0
Heterogen Atoms 43
Solvent Atoms 508

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
CNS refinement version: 1.1