X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 298.0
Details 100mM sodium citrate, 5mM DTT, 100mM MgCl2, 16% PEG 3350, 2mM ATP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.31 α = 90
b = 66.78 β = 90
c = 119.55 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 130
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-07-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 0.97 NSLS X25

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 99.8 -- -- -- -- -- 25287 -- -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 99.2 -- -- -- -- --

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
SAD 2.0 44.538 -- 0.21 -- 24992 1977 98.83 -- 0.1797 0.1753 0.2299 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 2.0 2.0496 -- 136 1540 0.2346 0.3519 -- 93.0
X Ray Diffraction 2.0496 2.105 -- 136 1578 0.2103 0.2958 -- 97.0
X Ray Diffraction 2.105 2.167 -- 140 1608 0.1906 0.2537 -- 98.0
X Ray Diffraction 2.167 2.2369 -- 136 1610 0.1753 0.2288 -- 99.0
X Ray Diffraction 2.2369 2.3169 -- 136 1611 0.1718 0.277 -- 99.0
X Ray Diffraction 2.3169 2.4096 -- 141 1628 0.1866 0.2549 -- 99.0
X Ray Diffraction 2.4096 2.5193 -- 141 1658 0.1937 0.2764 -- 100.0
X Ray Diffraction 2.5193 2.6521 -- 140 1623 0.1855 0.2548 -- 100.0
X Ray Diffraction 2.6521 2.8182 -- 142 1648 0.1768 0.2229 -- 100.0
X Ray Diffraction 2.8182 3.0358 -- 143 1665 0.1847 0.2414 -- 100.0
X Ray Diffraction 3.0358 3.3412 -- 143 1663 0.1779 0.2366 -- 100.0
X Ray Diffraction 3.3412 3.8245 -- 144 1677 0.1676 0.1979 -- 100.0
X Ray Diffraction 3.8245 4.8175 -- 146 1706 0.1341 0.1758 -- 100.0
X Ray Diffraction 4.8175 44.5492 -- 153 1800 0.1661 0.1807 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] 0.1328
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.8749
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.0077
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.071
f_dihedral_angle_d 16.638
f_angle_d 1.222
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2738
Nucleic Acid Atoms 0
Heterogen Atoms 78
Solvent Atoms 188

Software

Computing
Computing Package Purpose
CBASS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7.3_928) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7.3_928) refinement
PHENIX model building
CBASS data collection