X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 2.0 M ammonium sulfate, 0.1 M bis-tris, protein concentration = 7 mg/mL, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.01 α = 90
b = 45.01 β = 90
c = 113.44 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ mirrors 2010-03-22
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.62 35.26 99.5 0.068 -- -- 6.25 15533 15533 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)
1.62 1.68 96.0 0.363 -- 3.5 4.29 --

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 1.62 35.258 -- 1.37 15497 15504 1086 99.52 -- 0.1673 0.166 0.1843 --
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 1.62 1.6937 -- 128 1700 0.3527 0.3405 -- 97.0
X Ray Diffraction 1.6937 1.783 -- 133 1771 0.23 0.2901 -- 100.0
X Ray Diffraction 1.783 1.8947 -- 134 1776 0.1506 0.1954 -- 100.0
X Ray Diffraction 1.8947 2.041 -- 133 1775 0.1451 0.1699 -- 100.0
X Ray Diffraction 2.041 2.2464 -- 135 1786 0.1626 0.1922 -- 100.0
X Ray Diffraction 2.2464 2.5714 -- 136 1801 0.1594 0.1899 -- 100.0
X Ray Diffraction 2.5714 3.2393 -- 138 1846 0.1551 0.1711 -- 100.0
X Ray Diffraction 3.2393 35.2668 -- 149 1963 0.1526 0.1527 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -1.4738
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.4738
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 2.9475
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.074
f_plane_restr 0.004
f_angle_d 1.074
f_dihedral_angle_d 21.086
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1077
Nucleic Acid Atoms 0
Heterogen Atoms 55
Solvent Atoms 115

Software

Software
Software Name Purpose
d*TREK data scaling version: 9.9.8.6D
PHENIX refinement version: 1.6.4_486
PDB_EXTRACT data extraction version: 3.10
CrystalClear data collection
d*TREK data reduction
BALBES phasing
MOLREP phasing