X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 290.0
Details MCSG-1 d7 274321d7: 0.1 M sodium citrate/citric acid, pH 6.5, 40% PEG300, 4 mM NAD, 4 mM NADP, pH 6.5, cryoprotectant: 20% ethylene glycol, BupsA.00010.b.B1.PS00034 at 18.8 mg/mL, puck bsa9-6

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.49 α = 90
b = 119.35 β = 90
c = 135.9 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2016-07-05
Diffraction Radiation
Monochromator Protocol
diamond(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-G 0.97872 APS 21-ID-G

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 44.38 99.9 0.078 -- -- 6.08 -- 88784 -- -3.0 18.82
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 1.9 100.0 0.521 -- 3.35 -- --

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 1.85 38.181 -- 1.34 -- 88760 2106 99.9 -- 0.1457 0.145 0.1763 --
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 1.85 1.893 -- 135 5697 0.1917 0.2629 -- 100.0
X Ray Diffraction 1.893 1.9403 -- 138 5733 0.1852 0.2351 -- 100.0
X Ray Diffraction 1.9403 1.9928 -- 144 5710 0.1804 0.2205 -- 100.0
X Ray Diffraction 1.9928 2.0514 -- 149 5721 0.1652 0.2025 -- 100.0
X Ray Diffraction 2.0514 2.1176 -- 156 5686 0.1592 0.2063 -- 100.0
X Ray Diffraction 2.1176 2.1933 -- 143 5718 0.1509 0.1926 -- 100.0
X Ray Diffraction 2.1933 2.2811 -- 136 5739 0.1501 0.1714 -- 100.0
X Ray Diffraction 2.2811 2.3849 -- 118 5768 0.1531 0.206 -- 100.0
X Ray Diffraction 2.3849 2.5106 -- 131 5750 0.1558 0.1819 -- 100.0
X Ray Diffraction 2.5106 2.6679 -- 171 5742 0.1458 0.1867 -- 100.0
X Ray Diffraction 2.6679 2.8738 -- 136 5777 0.1461 0.1814 -- 100.0
X Ray Diffraction 2.8738 3.1629 -- 127 5818 0.1433 0.1672 -- 100.0
X Ray Diffraction 3.1629 3.6203 -- 143 5816 0.1308 0.18 -- 100.0
X Ray Diffraction 3.6203 4.56 -- 131 5893 0.1182 0.1315 -- 100.0
X Ray Diffraction 4.56 38.1891 -- 148 6086 0.1395 0.145 -- 99.0
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 8.884
f_angle_d 0.778
f_chiral_restr 0.051
f_plane_restr 0.005
f_bond_d 0.006
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7482
Nucleic Acid Atoms 0
Heterogen Atoms 212
Solvent Atoms 942

Software

Software
Software Name Purpose
PHENIX refinement version: (1.11rc3_2553: ???)
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.20
XDS data reduction
MoRDa phasing