X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 290.0
Details Microlytic MCSG1 condition E12: 2400mM Sodium malonate dibasic pH 7.0: ElmeA.00686.a.B1.PW38399 at 19.3mg/ml: cryo: direct: tray 299159e12: puck dod0-8

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.8 α = 90
b = 68.56 β = 118.66
c = 97.22 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-300 -- 2018-04-19
Diffraction Radiation
Monochromator Protocol
C(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F

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
2.1 47.9 97.8 0.059 -- -- 3.457 -- 31772 -- -- 37.268
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)
2.1 2.15 86.2 0.337 -- 2.58 2.343 --

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 2.1 47.895 -- 1.36 -- 31762 1955 98.0 -- 0.1744 0.1711 0.225 --
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 2.1 2.1525 -- 128 1832 0.2377 0.3007 0.0 86.0
X Ray Diffraction 2.1525 2.2107 -- 172 1995 0.213 0.2442 0.0 94.0
X Ray Diffraction 2.2107 2.2758 -- 143 2138 0.19 0.2425 0.0 99.0
X Ray Diffraction 2.2758 2.3492 -- 134 2172 0.1912 0.2825 0.0 100.0
X Ray Diffraction 2.3492 2.4332 -- 123 2154 0.1839 0.2646 0.0 100.0
X Ray Diffraction 2.4332 2.5306 -- 160 2136 0.1824 0.274 0.0 100.0
X Ray Diffraction 2.5306 2.6458 -- 167 2138 0.193 0.2791 0.0 100.0
X Ray Diffraction 2.6458 2.7853 -- 158 2150 0.1983 0.2218 0.0 99.0
X Ray Diffraction 2.7853 2.9597 -- 144 2146 0.2066 0.2816 0.0 100.0
X Ray Diffraction 2.9597 3.1882 -- 105 2194 0.1937 0.2638 0.0 100.0
X Ray Diffraction 3.1882 3.509 -- 123 2178 0.1752 0.2198 0.0 99.0
X Ray Diffraction 3.509 4.0165 -- 110 2185 0.143 0.1758 0.0 99.0
X Ray Diffraction 4.0165 5.0595 -- 139 2171 0.1302 0.1993 0.0 99.0
X Ray Diffraction 5.0595 47.9071 -- 149 2218 0.1582 0.171 0.0 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.2869
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.005
f_dihedral_angle_d 14.831
f_bond_d 0.007
f_angle_d 0.818
f_chiral_restr 0.048
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3454
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 246

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement version: (dev_3339)
PDB_EXTRACT data extraction version: 3.24
MoRDa phasing
PHASER phasing
PARROT phasing
Coot model building