X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6YVA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52890.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100
Crystal Properties
Matthews coefficientSolvent content
3.7166.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.673α = 90
b = 220.87β = 90
c = 232.787γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 X 6M2021-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9792APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
12.9848.9999.90.2140.2320.0890.9855.36.778254
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.033.081002.182.3610.90.3641.236.9

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 REPLACEMENTTHROUGHOUT6YVA2.9848.9974428378697.150.19710.19510.2358RANDOM76.102
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]
2.35-1.64-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.302
r_dihedral_angle_4_deg20.053
r_dihedral_angle_3_deg16.544
r_dihedral_angle_1_deg6.51
r_angle_refined_deg1.283
r_angle_other_deg1.089
r_chiral_restr0.042
r_bond_refined_d0.004
r_bond_other_d0.003
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.302
r_dihedral_angle_4_deg20.053
r_dihedral_angle_3_deg16.544
r_dihedral_angle_1_deg6.51
r_angle_refined_deg1.283
r_angle_other_deg1.089
r_chiral_restr0.042
r_bond_refined_d0.004
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18418
Nucleic Acid Atoms
Solvent Atoms54
Heterogen Atoms5

Software

Software
Software NamePurpose
HKL-3000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000phasing