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 = 156.54 α = 90
b = 156.54 β = 90
c = 156.54 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 2006-11-22
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 50 100.0 0.062 0.062 -- 22.6 -- 43061 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)
2.0 2.03 100.0 0.461 0.461 8.185 20.8 --

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 2.001 39.136 -- 0.0 -- 42998 2175 99.94 -- 0.1926 0.1914 0.2156 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 2.0011 2.0446 -- 137 2541 0.2234 0.2689 -- 100.0
X Ray Diffraction 2.0446 2.0921 -- 143 2528 0.2024 0.2548 -- 100.0
X Ray Diffraction 2.0921 2.1444 -- 150 2548 0.1998 0.246 -- 100.0
X Ray Diffraction 2.1444 2.2024 -- 117 2522 0.1928 0.2274 -- 100.0
X Ray Diffraction 2.2024 2.2672 -- 133 2527 0.1924 0.2505 -- 100.0
X Ray Diffraction 2.2672 2.3404 -- 109 2571 0.1989 0.2548 -- 100.0
X Ray Diffraction 2.3404 2.424 -- 141 2518 0.1979 0.2287 -- 100.0
X Ray Diffraction 2.424 2.5211 -- 135 2550 0.2006 0.2622 -- 100.0
X Ray Diffraction 2.5211 2.6358 -- 141 2525 0.2133 0.2542 -- 100.0
X Ray Diffraction 2.6358 2.7747 -- 135 2547 0.2082 0.252 -- 100.0
X Ray Diffraction 2.7747 2.9485 -- 127 2577 0.2051 0.2306 -- 100.0
X Ray Diffraction 2.9485 3.1761 -- 144 2527 0.205 0.2242 -- 100.0
X Ray Diffraction 3.1761 3.4955 -- 146 2552 0.2063 0.214 -- 100.0
X Ray Diffraction 3.4955 4.0009 -- 144 2546 0.1743 0.1908 -- 100.0
X Ray Diffraction 4.0009 5.039 -- 129 2609 0.1566 0.1446 -- 100.0
X Ray Diffraction 5.039 39.1435 -- 144 2635 0.1879 0.2108 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.0518
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 12.282
f_plane_restr 0.004
f_chiral_restr 0.068
f_angle_d 1.012
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3805
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 278

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