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 = 93.53 α = 90
b = 93.53 β = 90
c = 81.45 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
1.9 57.43 98.7 0.066 -- -- 7.13 31939 31524 -- -- --
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)
1.9 1.97 98.7 0.472 -- 3.0 6.96 3173

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 1.9001 36.263 -- 0.0 -- 31261 1572 97.87 -- 0.2176 0.2158 0.2508 --
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 1.9001 1.9614 -- 126 2632 0.3 0.3587 -- 95.0
X Ray Diffraction 1.9614 2.0315 -- 129 2713 0.2546 0.3244 -- 98.0
X Ray Diffraction 2.0315 2.1128 -- 147 2695 0.2354 0.3208 -- 99.0
X Ray Diffraction 2.1128 2.209 -- 143 2751 0.2341 0.2765 -- 99.0
X Ray Diffraction 2.209 2.3254 -- 127 2731 0.2323 0.2898 -- 100.0
X Ray Diffraction 2.3254 2.4711 -- 146 2742 0.2349 0.265 -- 99.0
X Ray Diffraction 2.4711 2.6618 -- 155 2732 0.2408 0.2823 -- 100.0
X Ray Diffraction 2.6618 2.9296 -- 145 2740 0.229 0.2829 -- 99.0
X Ray Diffraction 2.9296 3.3532 -- 167 2688 0.2142 0.2655 -- 98.0
X Ray Diffraction 3.3532 4.2237 -- 157 2613 0.1946 0.219 -- 95.0
X Ray Diffraction 4.2237 36.2696 -- 130 2652 0.2027 0.22 -- 94.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -5.0639
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.0639
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.1277
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.083
f_dihedral_angle_d 15.031
f_angle_d 1.299
f_bond_d 0.007
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2830
Nucleic Acid Atoms 0
Heterogen Atoms 118
Solvent Atoms 125

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