X-RAY DIFFRACTION Experimental Data & Validation


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Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 291.0
Details 3M NaCl, 0.1M Na Citrate pH6, 2.5% t-butanol, 20mM OBG, 5mM DTT, 3mM sodium azide, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 94.24 α = 90
b = 94.24 β = 90
c = 82.07 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX SX-165mm VariMax-HF --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418 -- --

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
1.93 57.9 99.8 0.04 -- -- 4.56 31178 31114 -- -- --
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)
1.93 2.0 99.8 0.317 -- 3.9 3.86 3068

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 1.9301 36.541 -- 0.0 -- 30772 1557 98.69 -- 0.2175 0.2159 0.247 --
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 1.9301 1.9924 -- 137 2540 0.3725 0.4339 -- 95.0
X Ray Diffraction 1.9924 2.0636 -- 145 2586 0.3287 0.3224 -- 97.0
X Ray Diffraction 2.0636 2.1462 -- 152 2614 0.2913 0.3157 -- 98.0
X Ray Diffraction 2.1462 2.2439 -- 134 2661 0.2582 0.2899 -- 99.0
X Ray Diffraction 2.2439 2.3622 -- 132 2669 0.2401 0.2761 -- 99.0
X Ray Diffraction 2.3622 2.5101 -- 133 2655 0.2461 0.2936 -- 99.0
X Ray Diffraction 2.5101 2.7039 -- 140 2686 0.2395 0.285 -- 100.0
X Ray Diffraction 2.7039 2.9759 -- 149 2681 0.219 0.2273 -- 100.0
X Ray Diffraction 2.9759 3.4062 -- 162 2683 0.2025 0.271 -- 100.0
X Ray Diffraction 3.4062 4.2904 -- 139 2713 0.1916 0.229 -- 100.0
X Ray Diffraction 4.2904 36.5474 -- 134 2727 0.1979 0.2028 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -2.5977
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.5977
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 5.1953
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.087
f_dihedral_angle_d 15.175
f_angle_d 1.374
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2834
Nucleic Acid Atoms 0
Heterogen Atoms 118
Solvent Atoms 109

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
d*TREK Data Reduction (intensity integration)
d*TREK Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHENIX model building
MAR345dtb data collection