X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details 31.5 % PEG 1000, 0.2 M Zn(CH3COO)2, 0.1 M CH3COONA PH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.25 α = 90
b = 80.16 β = 97.07
c = 72.14 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
CCD MAR scanner 300 mm plate -- 2009-04-02
Diffraction Radiation
Monochromator Protocol
SI (220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-BM 1.000 APS 22-BM

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
1.98 50 96.7 -- 0.081 -- -- -- 26922 -- 5.0 29.3
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)
1.98 2.05 86.9 -- 0.342 5.2 -- --

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 1.99 27.1 -- 0.05 -- 25977 1916 92.0 -- 0.18 0.177 0.215 --
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 1.988 2.038 -- 89 1125 0.223 0.311 -- 60.0
X Ray Diffraction 2.038 2.093 -- 123 1547 0.199 0.258 -- 84.0
X Ray Diffraction 2.093 2.155 -- 127 1678 0.196 0.269 -- 90.0
X Ray Diffraction 2.155 2.224 -- 142 1703 0.204 0.257 -- 92.0
X Ray Diffraction 2.224 2.304 -- 133 1721 0.203 0.314 -- 93.0
X Ray Diffraction 2.304 2.396 -- 145 1773 0.197 0.248 -- 95.0
X Ray Diffraction 2.396 2.505 -- 146 1769 0.201 0.293 -- 95.0
X Ray Diffraction 2.505 2.637 -- 134 1771 0.205 0.253 -- 95.0
X Ray Diffraction 2.637 2.802 -- 141 1801 0.202 0.253 -- 96.0
X Ray Diffraction 2.802 3.018 -- 147 1839 0.197 0.246 -- 98.0
X Ray Diffraction 3.018 3.321 -- 147 1819 0.171 0.19 -- 98.0
X Ray Diffraction 3.321 3.801 -- 146 1825 0.154 0.219 -- 98.0
X Ray Diffraction 3.801 4.784 -- 147 1838 0.138 0.156 -- 98.0
X Ray Diffraction 4.784 27.098 -- 149 1852 0.173 0.18 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 41.75
Anisotropic B[1][1] 7.708
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.834
Anisotropic B[2][2] 0.711
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.419
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.051
f_dihedral_angle_d 15.031
f_angle_d 0.768
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3402
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 331

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
PHASER Structure Solution
PHENIX (PHENIX.REFINE) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
phenix refinement