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 = 50.49 α = 90
b = 51 β = 90
c = 118.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 116
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2001-10-24
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
1.65 100 91.2 0.044 0.051 -- 11.74 -- 34532 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)
1.65 1.68 86.8 0.127 0.121 11.36 4.67 1614

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 1.65 50.0 0.0 0.0 37716 34380 1741 91.2 -- -- 0.1831 0.2151 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 1.65 1.71 3057 160 -- 0.3052 0.2713 -- 8.891
X Ray Diffraction 1.71 1.78 3059 179 -- 0.2459 0.2636 -- 8.897
X Ray Diffraction 1.78 1.86 3097 141 -- 0.1972 0.203 -- 9.008
X Ray Diffraction 1.86 1.96 3119 179 -- 0.1985 0.2428 -- 9.072
X Ray Diffraction 1.96 2.08 3190 174 -- 0.1841 0.2087 -- 9.27
X Ray Diffraction 2.08 2.24 3273 153 -- 0.1874 0.2138 -- 9.52
X Ray Diffraction 2.24 2.46 3291 185 -- 0.1868 0.227 -- 9.57
X Ray Diffraction 2.46 2.82 3420 195 -- 0.1876 0.234 -- 9.94
X Ray Diffraction 2.82 3.55 3507 185 -- 0.1639 0.188 -- 10.2
X Ray Diffraction 3.55 50.0 3626 190 -- 0.1615 0.1989 -- 10.54
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 18.5538
RMS Deviations
Key Refinement Restraint Deviation
c_angle_d 1.18
o_bond_d 0.0048
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2384
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 506

Software

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