X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5CGV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291.15MPD, PEG 1000, PEG 3350, Sodium HEPES, MOPS (acid), Magnesium chloride, Calcium chloride
Crystal Properties
Matthews coefficientSolvent content
2.3447.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.069α = 90
b = 74.069β = 90
c = 127.715γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2020-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54187

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
1242.5793.80.0310.034127.745.2332483341.742
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.1276.60.5080.6330.6881.642.324

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5CGV242.571326669995.360.20530.20230.2639RANDOM43.244
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.924
r_dihedral_angle_4_deg17.094
r_dihedral_angle_3_deg16.193
r_dihedral_angle_1_deg6.136
r_angle_refined_deg1.693
r_angle_other_deg1.055
r_chiral_restr0.095
r_bond_refined_d0.015
r_bond_other_d0.007
r_gen_planes_refined0.007
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.924
r_dihedral_angle_4_deg17.094
r_dihedral_angle_3_deg16.193
r_dihedral_angle_1_deg6.136
r_angle_refined_deg1.693
r_angle_other_deg1.055
r_chiral_restr0.095
r_bond_refined_d0.015
r_bond_other_d0.007
r_gen_planes_refined0.007
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1440
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing