3OYI

Crystal structure of the PFV S217Q mutant intasome in complex with manganese


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OY9PDB entry 3OY9

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
3.9869.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.58α = 90
b = 160.58β = 90
c = 123.46γ = 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
12.7238.94699.60.1466.44.643629-3-3
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)
2.722.8799.90.8640.8641.64.66310

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 3OY92.7238.9543445218599.060.220.21240.21080.2427RANDOM62.1283
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]
2.292.29-4.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.694
r_dihedral_angle_3_deg17.26
r_dihedral_angle_4_deg17.229
r_dihedral_angle_1_deg6.139
r_scangle_it2.94
r_scbond_it1.713
r_angle_refined_deg1.626
r_mcangle_it1.323
r_mcbond_it0.687
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.694
r_dihedral_angle_3_deg17.26
r_dihedral_angle_4_deg17.229
r_dihedral_angle_1_deg6.139
r_scangle_it2.94
r_scbond_it1.713
r_angle_refined_deg1.626
r_mcangle_it1.323
r_mcbond_it0.687
r_chiral_restr0.087
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4332
Nucleic Acid Atoms732
Solvent Atoms205
Heterogen Atoms38

Software

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