X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 20% PEG 3350, 0.2M NaF, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.93 α = 90
b = 70.21 β = 90.05
c = 84.01 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ BLUE CONFOCAL MIRRORS 2005-06-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.7 36 93.6 0.054 -- -- 8.4 -- 82678 0.0 0.0 --
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 89.3 0.537 -- -- 8.1 3910

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 35.882 -- 1.39 82662 82662 2599 93.5 -- 0.1696 0.1695 0.1825 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 1.7322 -- 125 4157 0.2812 0.344 -- 86.0
X Ray Diffraction 1.7322 1.7676 -- 137 4260 0.2529 0.2512 -- 87.0
X Ray Diffraction 1.7676 1.806 -- 127 4276 0.2294 0.2266 -- 88.0
X Ray Diffraction 1.806 1.848 -- 131 4334 0.2181 0.2875 -- 88.0
X Ray Diffraction 1.848 1.8943 -- 128 4328 0.2119 0.2132 -- 89.0
X Ray Diffraction 1.8943 1.9455 -- 134 4320 0.1894 0.2124 -- 89.0
X Ray Diffraction 1.9455 2.0027 -- 135 4372 0.1869 0.1868 -- 89.0
X Ray Diffraction 2.0027 2.0673 -- 132 4382 0.1884 0.2161 -- 90.0
X Ray Diffraction 2.0673 2.1412 -- 149 4426 0.1873 0.1957 -- 90.0
X Ray Diffraction 2.1412 2.2269 -- 138 4430 0.1836 0.1983 -- 91.0
X Ray Diffraction 2.2269 2.3282 -- 134 4500 0.177 0.1816 -- 92.0
X Ray Diffraction 2.3282 2.4509 -- 143 4463 0.1776 0.1967 -- 92.0
X Ray Diffraction 2.4509 2.6044 -- 150 4565 0.1738 0.1977 -- 92.0
X Ray Diffraction 2.6044 2.8054 -- 142 4566 0.1704 0.2071 -- 93.0
X Ray Diffraction 2.8054 3.0876 -- 135 4609 0.1649 0.1742 -- 94.0
X Ray Diffraction 3.0876 3.5339 -- 143 4625 0.1541 0.1454 -- 94.0
X Ray Diffraction 3.5339 4.4505 -- 149 4699 0.1315 0.1316 -- 95.0
X Ray Diffraction 4.4505 32.3971 -- 155 4830 0.1407 0.1668 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.477
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.074
f_plane_restr 0.003
f_chiral_restr 0.059
f_angle_d 0.864
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6144
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 971

Software

Computing
Computing Package Purpose
StructureStudio Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1186) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction