X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6DBA6DBA, 2UZX
experimental modelPDB 2UZX6DBA, 2UZX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52980.1 M Sodium Citrate Tribasic Dihydrate, 34 % Jeffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.1743.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.89α = 116.67
b = 66.95β = 97.73
c = 73.83γ = 95.08
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips2017-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97950CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5143.20193.5115.912.9122420
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.56

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6DBA, 2UZX1.5143.2011.97122399612193.520.16140.16040.180425.8283
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.794
f_angle_d1.099
f_chiral_restr0.064
f_bond_d0.012
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6203
Nucleic Acid Atoms
Solvent Atoms1085
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
pointlessdata scaling
PHENIXphasing