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, potassium phosphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.01 α = 90
b = 76.09 β = 90
c = 51.12 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Mirrors 2000-11-03
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 1.5418 -- --

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 50 -- 0.046 -- -- 9.142 -- 46346 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)
1.7 1.73 90.1 0.207 0.189 4.9756 4.41 2045

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 50.0 2.0 2.0 45673 43404 2269 97.9 -- -- 0.1859 0.2072 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 1.7 1.76 3832 184 -- 0.3505 0.3202 -- --
X Ray Diffraction 1.76 1.83 4244 204 -- 0.2653 0.2686 -- --
X Ray Diffraction 1.83 1.91 4283 211 -- 0.2022 0.2314 -- --
X Ray Diffraction 1.91 2.02 4354 211 -- 0.1751 0.1876 -- --
X Ray Diffraction 2.02 2.14 4352 252 -- 0.1707 0.2071 -- --
X Ray Diffraction 2.14 2.31 4397 237 -- 0.1699 0.1949 -- --
X Ray Diffraction 2.31 2.54 4395 242 -- 0.1808 0.2093 -- --
X Ray Diffraction 2.54 2.91 4424 232 -- 0.1701 0.2179 -- --
X Ray Diffraction 2.91 3.66 4502 240 -- 0.1788 0.2018 -- --
X Ray Diffraction 3.66 50.0 4621 256 -- 0.1811 0.1888 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
RMS Deviations
Key Refinement Restraint Deviation
c_angle_d 1.2576
o_bond_d 0.0076
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.02
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) -0.03
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2374
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 620

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection