X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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 = 93.67 α = 90
b = 93.67 β = 90
c = 81.83 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate 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
2.3 57.61 98.9 0.12 -- -- 8.28 18198 17994 -- -- --
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)
2.3 2.38 98.9 0.541 -- 2.8 8.49 1797

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 2.3001 46.836 -- 0.0 -- 17937 916 98.54 -- 0.1997 0.1971 0.2483 --
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 2.3001 2.4214 -- 145 2402 0.2417 0.3152 -- 99.0
X Ray Diffraction 2.4214 2.5731 -- 123 2442 0.2302 0.2884 -- 100.0
X Ray Diffraction 2.5731 2.7717 -- 135 2464 0.2222 0.315 -- 100.0
X Ray Diffraction 2.7717 3.0506 -- 138 2441 0.2081 0.2607 -- 100.0
X Ray Diffraction 3.0506 3.4919 -- 142 2455 0.1917 0.2646 -- 100.0
X Ray Diffraction 3.4919 4.3989 -- 132 2384 0.1666 0.2051 -- 97.0
X Ray Diffraction 4.3989 46.8452 -- 101 2433 0.2024 0.2383 -- 95.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -6.8012
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.8012
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.6024
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.082
f_dihedral_angle_d 15.408
f_angle_d 1.27
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2832
Nucleic Acid Atoms 0
Heterogen Atoms 117
Solvent Atoms 90

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