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 = 157.02 α = 90
b = 157.02 β = 90
c = 157.02 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
1.75 50 99.9 0.046 0.046 -- 16.8 -- 64664 0.0 -3.0 --
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)
1.75 1.78 100.0 0.474 0.474 6.643 16.8 --

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 1.75 35.11 -- 0.0 -- 64597 3256 99.92 -- 0.1899 0.1888 0.211 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 1.75 1.7762 -- 151 2635 0.2202 0.2683 -- 100.0
X Ray Diffraction 1.7762 1.8039 -- 147 2651 0.2197 0.2521 -- 100.0
X Ray Diffraction 1.8039 1.8335 -- 126 2713 0.2169 0.2556 -- 100.0
X Ray Diffraction 1.8335 1.8651 -- 133 2623 0.2185 0.2728 -- 100.0
X Ray Diffraction 1.8651 1.899 -- 146 2635 0.2143 0.271 -- 100.0
X Ray Diffraction 1.899 1.9355 -- 125 2659 0.1985 0.2447 -- 100.0
X Ray Diffraction 1.9355 1.975 -- 139 2660 0.2092 0.2403 -- 100.0
X Ray Diffraction 1.975 2.018 -- 153 2639 0.1922 0.2247 -- 100.0
X Ray Diffraction 2.018 2.0649 -- 136 2656 0.1898 0.1959 -- 100.0
X Ray Diffraction 2.0649 2.1165 -- 162 2647 0.1831 0.1884 -- 100.0
X Ray Diffraction 2.1165 2.1738 -- 143 2642 0.1942 0.2279 -- 100.0
X Ray Diffraction 2.1738 2.2377 -- 126 2674 0.1871 0.2693 -- 100.0
X Ray Diffraction 2.2377 2.3099 -- 129 2688 0.1905 0.2027 -- 100.0
X Ray Diffraction 2.3099 2.3925 -- 130 2660 0.1927 0.228 -- 100.0
X Ray Diffraction 2.3925 2.4882 -- 144 2650 0.1922 0.2238 -- 100.0
X Ray Diffraction 2.4882 2.6014 -- 155 2653 0.1987 0.238 -- 100.0
X Ray Diffraction 2.6014 2.7385 -- 149 2666 0.2 0.214 -- 100.0
X Ray Diffraction 2.7385 2.9101 -- 132 2676 0.1949 0.2275 -- 100.0
X Ray Diffraction 2.9101 3.1346 -- 140 2697 0.1973 0.2122 -- 100.0
X Ray Diffraction 3.1346 3.4498 -- 150 2650 0.1986 0.2264 -- 100.0
X Ray Diffraction 3.4498 3.9484 -- 154 2702 0.1756 0.1898 -- 100.0
X Ray Diffraction 3.9484 4.9723 -- 131 2723 0.1544 0.143 -- 100.0
X Ray Diffraction 4.9723 35.1169 -- 155 2742 0.189 0.209 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.7731
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 12.669
f_plane_restr 0.008
f_chiral_restr 0.107
f_angle_d 1.517
f_bond_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3783
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 315

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
pdb_extract version: 3.10 data extraction
phenix refinement
MOLREP molecular replacement
HKL data reduction