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 12% PEG 3350, 0.12M Mg-Formate, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 68.85 α = 90
b = 70.18 β = 90
c = 83.73 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
1.78 32 97.1 0.059 -- -- 7.3 -- 74257 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)
1.78 1.81 83.1 0.335 -- -- 5.9 3178

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 1.78 25.05 -- 1.38 74239 74239 2564 97.06 -- 0.1642 0.1633 0.1807 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 1.78 1.8147 -- 125 3408 0.2922 0.3263 -- 80.0
X Ray Diffraction 1.8147 1.8517 -- 123 3698 0.2556 0.2481 -- 88.0
X Ray Diffraction 1.8517 1.8919 -- 137 3868 0.2209 0.2167 -- 92.0
X Ray Diffraction 1.8919 1.9359 -- 145 3931 0.196 0.2072 -- 93.0
X Ray Diffraction 1.9359 1.9842 -- 137 3952 0.1894 0.1886 -- 94.0
X Ray Diffraction 1.9842 2.0378 -- 139 3979 0.1839 0.1745 -- 94.0
X Ray Diffraction 2.0378 2.0977 -- 144 3973 0.1828 0.2244 -- 94.0
X Ray Diffraction 2.0977 2.1654 -- 136 3988 0.1769 0.1955 -- 95.0
X Ray Diffraction 2.1654 2.2426 -- 150 4010 0.1761 0.1951 -- 95.0
X Ray Diffraction 2.2426 2.3323 -- 141 4035 0.1658 0.1511 -- 95.0
X Ray Diffraction 2.3323 2.4382 -- 136 4065 0.1694 0.2209 -- 95.0
X Ray Diffraction 2.4382 2.5665 -- 145 4019 0.167 0.2042 -- 95.0
X Ray Diffraction 2.5665 2.7269 -- 139 4085 0.163 0.1631 -- 96.0
X Ray Diffraction 2.7269 2.9368 -- 140 4072 0.1596 0.1715 -- 96.0
X Ray Diffraction 2.9368 3.2311 -- 147 4112 0.1594 0.1822 -- 96.0
X Ray Diffraction 3.2311 3.6958 -- 145 4127 0.1475 0.1566 -- 96.0
X Ray Diffraction 3.6958 4.6457 -- 148 4149 0.1203 0.154 -- 97.0
X Ray Diffraction 4.6457 19.3498 -- 149 4199 0.145 0.1648 -- 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 21.0129
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.796
f_plane_restr 0.004
f_chiral_restr 0.058
f_angle_d 0.877
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5985
Nucleic Acid Atoms 0
Heterogen Atoms 8
Solvent Atoms 649

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_1218) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction