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
c_angle_d 2.174
o_bond_d 0.0051
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 51
Solvent Atoms 500

Software

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