X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.4
Temperature 291.0
Details 50 mM Tris HCl pH=8.4, 0.2 M NH4Cl, 10 mM CaCl2, 34% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 109.21 α = 90
b = 109.21 β = 90
c = 91.05 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M Dynamically bendable mirror, LN2 cooled fixed-exit, Si(111) monochromator 2010-08-13
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit, Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA

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
1.89 50 99.3 0.118 -- -- -- 50305 50305 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)
1.89 2.0 95.6 1.182 -- 1.2 -- --

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
MOLECULAR REPLACEMENT 1.9 47.291 -- 2.0 49722 49722 2491 99.97 -- 0.1785 0.1765 0.2157 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 1.9 1.9366 -- 131 2582 0.2918 0.3147 -- 100.0
X Ray Diffraction 1.9366 1.9761 -- 141 2598 0.2523 0.2869 -- 100.0
X Ray Diffraction 1.9761 2.0191 -- 152 2622 0.2421 0.3034 -- 100.0
X Ray Diffraction 2.0191 2.066 -- 126 2568 0.2303 0.2411 -- 100.0
X Ray Diffraction 2.066 2.1177 -- 143 2607 0.2123 0.2428 -- 100.0
X Ray Diffraction 2.1177 2.1749 -- 122 2591 0.2056 0.23 -- 100.0
X Ray Diffraction 2.1749 2.2389 -- 120 2607 0.2042 0.2475 -- 100.0
X Ray Diffraction 2.2389 2.3112 -- 142 2616 0.1986 0.2593 -- 100.0
X Ray Diffraction 2.3112 2.3938 -- 118 2625 0.1782 0.238 -- 100.0
X Ray Diffraction 2.3938 2.4897 -- 129 2627 0.1735 0.2256 -- 100.0
X Ray Diffraction 2.4897 2.603 -- 146 2611 0.1703 0.219 -- 100.0
X Ray Diffraction 2.603 2.7402 -- 148 2604 0.1736 0.2299 -- 100.0
X Ray Diffraction 2.7402 2.9118 -- 138 2625 0.1869 0.2226 -- 100.0
X Ray Diffraction 2.9118 3.1366 -- 132 2640 0.1786 0.2613 -- 100.0
X Ray Diffraction 3.1366 3.4522 -- 150 2615 0.1624 0.1881 -- 100.0
X Ray Diffraction 3.4522 3.9515 -- 155 2644 0.1426 0.1787 -- 100.0
X Ray Diffraction 3.9515 4.9776 -- 141 2671 0.1391 0.1811 -- 100.0
X Ray Diffraction 4.9776 47.3052 -- 157 2778 0.1739 0.1915 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic and tls
Anisotropic B[1][1] 5.1587
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 5.1587
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.1226
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_chiral_restr 0.071
f_dihedral_angle_d 16.929
f_angle_d 1.172
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4286
Nucleic Acid Atoms 520
Heterogen Atoms 77
Solvent Atoms 323

Software

Computing
Computing Package Purpose
XDS Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHENIX (phenix.refine: dev_1009) Structure Solution
PHENIX (phenix.refine: dev_1009) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: dev_1009) refinement
PHENIX version: (phenix.refine: dev_1009) model building
XDS data collection