3OYM

Crystal structure of the PFV N224H mutant intasome bound to 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
3.8167.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 158.05α = 90
b = 158.05β = 90
c = 122.16γ = 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
12.0239.89498.90.1068.74.899967-3-3
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)
2.022.1398.80.7610.7611.64.914403

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 3OY92.0239.8999745502598.520.20.19870.19720.2276RANDOM37.6561
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]
1.091.09-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.347
r_dihedral_angle_4_deg14.443
r_dihedral_angle_3_deg14.05
r_dihedral_angle_1_deg5.81
r_scangle_it2.877
r_scbond_it1.773
r_angle_refined_deg1.353
r_mcangle_it1.259
r_mcbond_it0.662
r_chiral_restr0.078
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.347
r_dihedral_angle_4_deg14.443
r_dihedral_angle_3_deg14.05
r_dihedral_angle_1_deg5.81
r_scangle_it2.877
r_scbond_it1.773
r_angle_refined_deg1.353
r_mcangle_it1.259
r_mcbond_it0.662
r_chiral_restr0.078
r_bond_refined_d0.01
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4388
Nucleic Acid Atoms732
Solvent Atoms596
Heterogen Atoms58

Software

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