X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 285.0
Details Molecular Dimensions Morpheus screen, condition C4: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD 30mM each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate: 100mM MES/imidazole pH 6.5: LepnA.01206.a.B1.PS38438 at 24.33mg/ml: 2h soak with 5mM MgCl2 + dUTP with was converted to dUMP: cryo: direct: EG in two steps: tray 301633a1, puck PXP9-8

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 85.67 α = 90
b = 85.67 β = 90
c = 55.46 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944+ -- 2018-08-21
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418 -- --

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
1.95 37.1 100.0 0.059 -- -- 9.282 -- 17033 -- -- 34.444
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)
1.95 2.0 99.9 0.47 -- 3.04 5.22 --

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 1.95 37.096 -- 1.35 -- 17031 1774 99.97 -- 0.1515 0.1482 0.1811 --
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 1.95 2.0028 -- 136 1179 0.2104 0.2521 0.0 100.0
X Ray Diffraction 2.0028 2.0617 -- 129 1156 0.1801 0.2277 0.0 100.0
X Ray Diffraction 2.0617 2.1282 -- 146 1158 0.178 0.2021 0.0 100.0
X Ray Diffraction 2.1282 2.2043 -- 154 1148 0.1628 0.1852 0.0 100.0
X Ray Diffraction 2.2043 2.2925 -- 120 1171 0.1568 0.1879 0.0 100.0
X Ray Diffraction 2.2925 2.3968 -- 128 1180 0.1615 0.2036 0.0 100.0
X Ray Diffraction 2.3968 2.5232 -- 159 1151 0.1614 0.2252 0.0 100.0
X Ray Diffraction 2.5232 2.6812 -- 133 1177 0.1537 0.1961 0.0 100.0
X Ray Diffraction 2.6812 2.8882 -- 119 1171 0.1632 0.187 0.0 100.0
X Ray Diffraction 2.8882 3.1787 -- 123 1201 0.164 0.2062 0.0 100.0
X Ray Diffraction 3.1787 3.6383 -- 126 1180 0.1394 0.1871 0.0 100.0
X Ray Diffraction 3.6383 4.5825 -- 150 1175 0.116 0.1438 0.0 100.0
X Ray Diffraction 4.5825 37.1029 -- 151 1210 0.1365 0.1555 0.0 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.5277
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.933
f_bond_d 0.009
f_plane_restr 0.006
f_dihedral_angle_d 13.83
f_chiral_restr 0.074
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1044
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 138

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHENIX refinement version: (1.14_3211)
PDB_EXTRACT data extraction version: 3.24
PHASER phasing
Coot model building