3OYJ

Crystal structure of the PFV S217Q mutant intasome in complex with magnesium and the INSTI MK2048


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OYBPDB entry 3OYB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52911.35 M ammonium sulfate, 25% (v/v) glycerol, 4.8% (v/v) 1,6-hexanediol, 50 mM Mes-NaOH, 1mM EDTA, pH 6.5, vapor diffusion, hanging drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
3.9768.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.17α = 90
b = 160.17β = 90
c = 123.7γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-06-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97630DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (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
12.6839.18798.90.10111.25.545020-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.682.8298.90.8940.8941.65.56473

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3OYB2.6838.8544899226098.30.210.20740.20560.2408RANDOM62.2024
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]
0.450.45-0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.706
r_dihedral_angle_3_deg17.197
r_dihedral_angle_4_deg14.133
r_dihedral_angle_1_deg6.35
r_scangle_it2.964
r_scbond_it1.725
r_angle_refined_deg1.579
r_mcangle_it1.32
r_mcbond_it0.684
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.706
r_dihedral_angle_3_deg17.197
r_dihedral_angle_4_deg14.133
r_dihedral_angle_1_deg6.35
r_scangle_it2.964
r_scbond_it1.725
r_angle_refined_deg1.579
r_mcangle_it1.32
r_mcbond_it0.684
r_chiral_restr0.089
r_bond_refined_d0.012
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4345
Nucleic Acid Atoms732
Solvent Atoms198
Heterogen Atoms71

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection