X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.1
Temperature 293.0
Details 1:1.5 PROTEIN/DNA RATIO, 20% PEG 3350, 0.2M KCl, pH 6.1, Vapor diffusion, hanging drop, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.94 α = 90
b = 74.94 β = 90
c = 73.31 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4r TOROIDAL MIRROR 2006-04-27
Diffraction Radiation
Monochromator Protocol
DIAMOND (111), GE(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-3 0.9310 ESRF ID14-3

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 27 99.7 0.141 -- -- 5.1 -- 22336 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 1.81 100.0 0.529 -- -- 5.3 1116

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 24.529 -- 1.37 22322 22322 1107 99.69 -- 0.1632 0.1616 0.1937 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 1.8626 -- 133 2615 0.1999 0.272 -- 99.0
X Ray Diffraction 1.8626 1.9608 -- 136 2651 0.1831 0.2259 -- 100.0
X Ray Diffraction 1.9608 2.0836 -- 139 2666 0.1685 0.2183 -- 100.0
X Ray Diffraction 2.0836 2.2444 -- 138 2631 0.1619 0.2026 -- 100.0
X Ray Diffraction 2.2444 2.47 -- 139 2652 0.1681 0.2028 -- 100.0
X Ray Diffraction 2.47 2.827 -- 138 2670 0.1776 0.2148 -- 100.0
X Ray Diffraction 2.827 3.56 -- 143 2661 0.1525 0.1855 -- 100.0
X Ray Diffraction 3.56 24.5312 -- 141 2669 0.1388 0.148 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.3819
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.843
f_plane_restr 0.006
f_chiral_restr 0.094
f_angle_d 1.33
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1529
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 259

Software

Computing
Computing Package Purpose
DNA Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: dev_1223) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Phaser molecular replacement
HKL data reduction