X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 298.0
Details PEG 8000, MgCl, Tris, ZnCl, vapor diffusion, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.71 α = 90
b = 81.3 β = 90
c = 131.42 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2007-10-25
Diffraction Radiation
Monochromator Protocol
-- single wavelength
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE -- 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
1.65 19.92 95.9 0.05 -- -- 4.0 -- 57408 -- -- --
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)
1.65 1.71 97.6 0.253 -- 4.0 3.71 5748

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 1.65 19.92 -- 1.38 -- 57382 2915 95.78 -- 0.1772 0.1761 0.1978 --
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 1.649 1.676 -- 157 2551 0.2206 0.2634 -- 95.0
X Ray Diffraction 1.676 1.7049 -- 137 2580 0.2082 0.2453 -- 97.0
X Ray Diffraction 1.7049 1.7359 -- 158 2594 0.2029 0.2716 -- 97.0
X Ray Diffraction 1.7359 1.7693 -- 130 2610 0.207 0.2614 -- 97.0
X Ray Diffraction 1.7693 1.8053 -- 121 2601 0.2085 0.2753 -- 97.0
X Ray Diffraction 1.8053 1.8446 -- 125 2628 0.2103 0.2797 -- 98.0
X Ray Diffraction 1.8446 1.8875 -- 143 2597 0.1954 0.2666 -- 97.0
X Ray Diffraction 1.8875 1.9346 -- 141 2601 0.1909 0.2296 -- 97.0
X Ray Diffraction 1.9346 1.9869 -- 157 2631 0.19 0.2234 -- 97.0
X Ray Diffraction 1.9869 2.0453 -- 130 2579 0.1831 0.2192 -- 97.0
X Ray Diffraction 2.0453 2.1112 -- 132 2589 0.1783 0.24 -- 96.0
X Ray Diffraction 2.1112 2.1866 -- 121 2605 0.1824 0.1769 -- 96.0
X Ray Diffraction 2.1866 2.274 -- 138 2610 0.1709 0.1804 -- 96.0
X Ray Diffraction 2.274 2.3774 -- 148 2543 0.1734 0.1864 -- 95.0
X Ray Diffraction 2.3774 2.5025 -- 115 2572 0.1821 0.1819 -- 95.0
X Ray Diffraction 2.5025 2.6589 -- 146 2549 0.18 0.2083 -- 94.0
X Ray Diffraction 2.6589 2.8637 -- 148 2562 0.1756 0.2288 -- 94.0
X Ray Diffraction 2.8637 3.1509 -- 131 2577 0.1784 0.2028 -- 95.0
X Ray Diffraction 3.1509 3.6045 -- 142 2597 0.1719 0.1794 -- 94.0
X Ray Diffraction 3.6045 4.5324 -- 148 2619 0.1535 0.181 -- 94.0
X Ray Diffraction 4.5324 19.9235 -- 147 2672 0.1696 0.1578 -- 92.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 29.158
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 12.223
f_plane_restr 0.005
f_chiral_restr 0.073
f_angle_d 1.48
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3314
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 585

Software

Computing
Computing Package Purpose
d*TREK Data Reduction (intensity integration)
DTREK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.8.1_1168) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
D*trek version: 9.4SSI data reduction