X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 295.0
Details 5-7% PEG 3000, 0.1M MES pH 6.1-6.3, 0.3M LiCl, 10mM MgCl2, vapor diffusion, hanging drop, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 286.55 α = 90
b = 286.55 β = 90
c = 199.41 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2011-11-04
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.91956 APS 24-ID-C

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
4 45 99.5 0.442 -- -- 5.9 52138 51877 2.0 2.0 --
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)
4.0 4.07 97.7 -- -- -- 4.8 --

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 4.2927 38.785 -- 1.96 41681 41266 2070 99.01 -- 0.237 0.2345 0.2849 --
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 4.2927 4.3925 -- 150 2516 0.3463 0.364 -- 95.0
X Ray Diffraction 4.3925 4.5022 -- 153 2579 0.3317 0.3291 -- 99.0
X Ray Diffraction 4.5022 4.6237 -- 117 2639 0.3042 0.335 -- 99.0
X Ray Diffraction 4.6237 4.7595 -- 164 2585 0.2861 0.3725 -- 99.0
X Ray Diffraction 4.7595 4.9129 -- 146 2624 0.2845 0.2951 -- 99.0
X Ray Diffraction 4.9129 5.0881 -- 135 2641 0.2736 0.2978 -- 100.0
X Ray Diffraction 5.0881 5.2913 -- 124 2622 0.2761 0.2888 -- 99.0
X Ray Diffraction 5.2913 5.5315 -- 135 2626 0.2746 0.3372 -- 100.0
X Ray Diffraction 5.5315 5.8222 -- 133 2639 0.2716 0.3669 -- 99.0
X Ray Diffraction 5.8222 6.1856 -- 146 2624 0.2603 0.3049 -- 100.0
X Ray Diffraction 6.1856 6.661 -- 151 2618 0.2418 0.3088 -- 100.0
X Ray Diffraction 6.661 7.3273 -- 143 2649 0.2145 0.2744 -- 100.0
X Ray Diffraction 7.3273 8.3782 -- 126 2598 0.1893 0.2551 -- 99.0
X Ray Diffraction 8.3782 10.5207 -- 124 2648 0.1802 0.2351 -- 99.0
X Ray Diffraction 10.5207 38.7867 -- 123 2588 0.2142 0.2513 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 125.919
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.061
f_dihedral_angle_d 16.343
f_angle_d 0.934
f_bond_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 23534
Nucleic Acid Atoms 863
Heterogen Atoms 3
Solvent Atoms 0

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL Data Reduction (intensity integration)
HKL Data Reduction (data scaling)
CNS Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
CNS molecular replacement
HKL data reduction