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 2376
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 506

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
XENGEN Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
AMoRE model building
XENGEN data reduction
DENZO data collection