X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Evaporation
pH 7.5
Temperature 277.0
Details 0.1 M HEPES sodium, pH 7.5, 1M Sodium citrate tribasic dihydrate, 10 mM TCEP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.52 α = 90
b = 51.52 β = 90
c = 335.68 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300-HS -- 2017-07-19
Diffraction Radiation
Monochromator Protocol
LN2-Cooled, Fixed-Exit Double Crystal Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSRRC BEAMLINE TPS 05A 1 NSRRC TPS 05A

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
2.6 44.62 99.81 0.05055 -- -- 1.96 -- 9019 -- -- 49.3
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)
2.6 2.693 99.88 0.4142 -- 2.17 -- --

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 2.6 44.616 -- 1.34 -- 9015 443 99.82 -- 0.1953 0.1929 0.2416 --
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 2.6 2.693 -- 131 2750 0.2471 0.2904 -- 100.0
X Ray Diffraction 2.693 3.7494 -- 151 2795 0.2038 0.2849 -- 100.0
X Ray Diffraction 3.7494 44.6224 -- 161 3027 0.1735 0.2066 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 46.2
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 1.012
f_dihedral_angle_d 9.515
f_plane_restr 0.006
f_chiral_restr 0.058
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1327
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 63

Software

Software
Software Name Purpose
Blu-Ice data collection
XDS data reduction
XSCALE data scaling
PHENIX model building
PHENIX refinement version: 1.12_2829