X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 298.0
Details 20% polyethylene glycol (PEG) 3350 (w/v), 0.05 M zinc acetate dihydrate, cryoprotectant paratone oil, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.64 α = 90
b = 83.64 β = 90
c = 50.58 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2014-06-09
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.12720 APS 21-ID-D

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
2.02 19.32 99.8 0.054 -- -- 8.1 -- 12161 0.0 -2.0 --
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)
2.02 2.22 99.6 0.478 -- 3.4 7.3 2827

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 2.025 19.323 -- 1.34 -- -- 1071 99.84 -- 0.1895 0.1885 0.2091 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 2.0247 2.1167 -- 149 2609 0.284 0.2956 -- 99.0
X Ray Diffraction 2.1167 2.2282 -- 124 2665 0.2574 0.2558 -- 100.0
X Ray Diffraction 2.2282 2.3676 -- 139 2643 0.2346 0.2842 -- 100.0
X Ray Diffraction 2.3676 2.55 -- 129 2656 0.245 0.2836 -- 100.0
X Ray Diffraction 2.55 2.8059 -- 127 2666 0.2427 0.2774 -- 100.0
X Ray Diffraction 2.8059 3.2103 -- 143 2649 0.2044 0.1962 -- 100.0
X Ray Diffraction 3.2103 4.0386 -- 121 2656 0.1764 0.2157 -- 100.0
X Ray Diffraction 4.0386 19.3236 -- 139 2652 0.1411 0.1578 -- 100.0
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.032
f_bond_d 0.007
f_angle_d 1.11
f_dihedral_angle_d 14.128
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1071
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 97

Software

Software
Software Name Purpose
HKL-3000 data collection
PHENIX model building version: (phenix.autsol)
PHENIX refinement version: (phenix.refine: 1.9_1692)
XDS data reduction
Aimless data scaling
PHENIX phasing