X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 291.0
Details see manuscript, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.93 α = 90
b = 90.93 β = 90
c = 54.08 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
STORAGE PHOSPHORS PSI PILATUS 6M mirrors 2012-09-17
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 DIAMOND I02

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
2.15 44.58 100.0 -- -- -- -- 14357 14357 0.0 0.0 --
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)
2.15 2.27 100.0 -- -- 2.3 -- --

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 2.15 44.58 -- 1.34 14328 14328 701 99.93 -- 0.1952 0.1946 0.2066 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 2.15 2.316 -- 145 2679 0.266 0.2902 -- 100.0
X Ray Diffraction 2.316 2.5491 -- 149 2683 0.2168 0.2416 -- 100.0
X Ray Diffraction 2.5491 2.9178 -- 123 2711 0.2145 0.2305 -- 100.0
X Ray Diffraction 2.9178 3.6759 -- 148 2724 0.2019 0.2261 -- 100.0
X Ray Diffraction 3.6759 44.5899 -- 136 2830 0.1748 0.1722 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_chiral_restr 0.043
f_dihedral_angle_d 14.125
f_angle_d 0.866
f_bond_d 0.003
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1024
Nucleic Acid Atoms 217
Heterogen Atoms 18
Solvent Atoms 25

Software

Computing
Computing Package Purpose
EDNA Data Collection
XDS Data Reduction (intensity integration)
AIMLESS Data Reduction (data scaling)
Phenix Structure Solution
PHENIX (phenix.refine: 1.8.2_1309) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.2_1309) refinement
Phenix model building
EDNA data collection