X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details 35% (v/v) glycerol ethoxylate, 75 mM sodium malonate, pH7.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.08 α = 90
b = 60.08 β = 90
c = 162.29 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
PIXEL DECTRIS PILATUS 2M-F -- 2018-08-24
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA

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
1.85 43.8 100.0 -- 0.088 -- 19.3 -- 29819 -- -- --
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)
1.85 1.96 99.7 -- 2.706 -- 18.9 --

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 1.851 43.799 -- 1.35 -- 29819 1508 99.95 -- 0.1962 0.1946 0.2258 --
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 1.8513 1.9111 -- 136 2513 0.3264 0.3762 -- 99.0
X Ray Diffraction 1.9111 1.9794 -- 134 2506 0.297 0.3388 -- 100.0
X Ray Diffraction 1.9794 2.0586 -- 136 2551 0.2757 0.2977 -- 100.0
X Ray Diffraction 2.0586 2.1523 -- 138 2531 0.2476 0.3226 -- 100.0
X Ray Diffraction 2.1523 2.2658 -- 137 2542 0.2315 0.28 -- 100.0
X Ray Diffraction 2.2658 2.4077 -- 135 2569 0.2242 0.2671 -- 100.0
X Ray Diffraction 2.4077 2.5936 -- 137 2539 0.2173 0.2307 -- 100.0
X Ray Diffraction 2.5936 2.8546 -- 133 2578 0.2038 0.2415 -- 100.0
X Ray Diffraction 2.8546 3.2675 -- 137 2586 0.2084 0.242 -- 100.0
X Ray Diffraction 3.2675 4.1163 -- 137 2620 0.1678 0.1985 -- 100.0
X Ray Diffraction 4.1163 43.811 -- 148 2776 0.1648 0.1882 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.059
f_plane_restr 0.006
f_dihedral_angle_d 23.449
f_bond_d 0.008
f_angle_d 0.948
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2800
Nucleic Acid Atoms 86
Heterogen Atoms 2
Solvent Atoms 130

Software

Software
Software Name Purpose
PHENIX refinement version: (1.14_3260: ???)
XDS data reduction
Coot model building
PHASER phasing
XSCALE data scaling