X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 25 mMTris-HCl containing 1 mM zinc sulfate at pH 7.0, and 25 mMTris-HCl with 1 mM zinc chloride at pH 7.0, and the mother liquor which consisted of 0.1 M tri-sodium citrate (pH 5.5) in 40% PEG 600., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.03 α = 90
b = 59.77 β = 90
c = 83.55 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS HTC -- 2010-01-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54 -- --

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
2 25.24 89.2 0.057 -- -- 4.04 15635 15635 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)
2.0 2.07 93.0 0.311 -- 3.1 3.86 --

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 2.0 25.24 -- 1.34 15635 15601 794 89.2 0.2013 0.2013 0.1988 0.2492 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 2.0 2.1253 -- 149 2485 0.2449 0.2836 -- 93.0
X Ray Diffraction 2.1253 2.2893 -- 131 2513 0.2183 0.2603 -- 92.0
X Ray Diffraction 2.2893 2.5195 -- 138 2481 0.2138 0.2919 -- 91.0
X Ray Diffraction 2.5195 2.8836 -- 130 2470 0.224 0.3314 -- 90.0
X Ray Diffraction 2.8836 3.6313 -- 133 2433 0.1898 0.2149 -- 88.0
X Ray Diffraction 3.6313 25.2469 -- 113 2425 0.1798 0.2213 -- 83.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -6.605
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 8.0412
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.4362
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.066
f_dihedral_angle_d 13.201
f_angle_d 1.044
f_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1737
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 151

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHASER model building
CrystalClear data collection