X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9.5
Temperature 298.0
Details 1M Sodium citrate, 0.1 M CHES pH9.5 diluted by water 4:1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.29 α = 90
b = 65.29 β = 90
c = 96.2 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- 2010-04-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-BM 0.97931 APS 19-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
1.8 100 99.8 0.04 -- -- 12.0 22646 22608 -- -3.0 22.3
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)
1.798 1.83 100.0 0.341 -- 6.4 12.0 1095

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 1.798 30.914 -- 1.34 22608 22528 1153 99.65 -- 0.1772 0.1748 0.2232 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 1.798 1.8803 -- 161 2609 0.1819 0.2295 -- 100.0
X Ray Diffraction 1.8803 1.9794 -- 132 2653 0.1833 0.2123 -- 100.0
X Ray Diffraction 1.9794 2.1034 -- 144 2643 0.1808 0.2329 -- 100.0
X Ray Diffraction 2.1034 2.2658 -- 139 2641 0.1729 0.2399 -- 100.0
X Ray Diffraction 2.2658 2.4937 -- 154 2643 0.1893 0.231 -- 100.0
X Ray Diffraction 2.4937 2.8543 -- 139 2675 0.1855 0.2336 -- 99.0
X Ray Diffraction 2.8543 3.5953 -- 130 2694 0.1715 0.2345 -- 99.0
X Ray Diffraction 3.5953 30.9182 -- 154 2817 0.1657 0.2043 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.1573
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.1573
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.3146
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.009
f_chiral_restr 0.118
f_dihedral_angle_d 16.917
f_angle_d 1.627
f_bond_d 0.016
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1724
Nucleic Acid Atoms 0
Heterogen Atoms 13
Solvent Atoms 203

Software

Computing
Computing Package Purpose
HKL-3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
Phaser Structure Solution
PHENIX (phenix.refine: 1.7.1_743) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.1_743) refinement
Phaser model building
HKL-3000 data collection