X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.2
Temperature 293.0
Details 0.1M ammonium sulfate, 24-32% PEG5000 monomethyl ether, 1mM ATP, 100mM Hepes buffer, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 156.15 α = 90
b = 156.15 β = 90
c = 156.15 γ = 90
Symmetry
Space Group I 2 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 mirrors 2006-12-14
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 SPRING-8 BL44B2

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
2.1 50 100.0 0.066 0.066 -- 15.1 -- 37003 0.0 -3.0 27.52
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)
2.1 2.14 100.0 0.405 0.405 7.878 15.1 --

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 2.1 34.915 -- 0.0 -- 36956 1853 99.91 -- 0.1858 0.184 0.221 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 2.1001 2.1569 -- 153 2684 0.1843 0.2558 -- 100.0
X Ray Diffraction 2.1569 2.2204 -- 125 2719 0.1907 0.2292 -- 100.0
X Ray Diffraction 2.2204 2.292 -- 124 2678 0.2117 0.2715 -- 100.0
X Ray Diffraction 2.292 2.3739 -- 127 2677 0.1914 0.2425 -- 100.0
X Ray Diffraction 2.3739 2.4689 -- 150 2682 0.1815 0.226 -- 100.0
X Ray Diffraction 2.4689 2.5813 -- 153 2652 0.1985 0.2865 -- 100.0
X Ray Diffraction 2.5813 2.7173 -- 152 2670 0.2032 0.272 -- 100.0
X Ray Diffraction 2.7173 2.8875 -- 132 2717 0.1962 0.2651 -- 100.0
X Ray Diffraction 2.8875 3.1103 -- 141 2692 0.2047 0.2246 -- 100.0
X Ray Diffraction 3.1103 3.4231 -- 153 2699 0.1999 0.2481 -- 100.0
X Ray Diffraction 3.4231 3.9178 -- 157 2703 0.1779 0.1946 -- 100.0
X Ray Diffraction 3.9178 4.9338 -- 131 2742 0.1489 0.165 -- 100.0
X Ray Diffraction 4.9338 34.9201 -- 155 2788 0.1777 0.1937 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.1802
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 13.699
f_plane_restr 0.006
f_chiral_restr 0.083
f_angle_d 1.3
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3805
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 281

Software

Computing
Computing Package Purpose
BSS Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Molrep Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
Molrep model building
BSS data collection