4LVK

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt+3'Phosphate). Mn-bound crystal structure at pH 4.6


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION + seeding4.629322% PEG 4000, 0.2M Sodium Chloride, 0.1M Sodium Acetate pH4.6., VAPOR DIFFUSION + seeding, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.743α = 90
b = 112.743β = 90
c = 91.66γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-06-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97300ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.373799.30.10712.28.413543-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.372.5197.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.3736.931354371598.710.203120.20070.24987RANDOM59.347
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]
2.282.282.28-7.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.301
r_dihedral_angle_4_deg18.581
r_dihedral_angle_3_deg16.715
r_dihedral_angle_1_deg6.173
r_mcangle_it2.965
r_scbond_it2.674
r_mcbond_it1.92
r_angle_refined_deg1.864
r_chiral_restr0.116
r_bond_refined_d0.012
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.301
r_dihedral_angle_4_deg18.581
r_dihedral_angle_3_deg16.715
r_dihedral_angle_1_deg6.173
r_mcangle_it2.965
r_scbond_it2.674
r_mcbond_it1.92
r_angle_refined_deg1.864
r_chiral_restr0.116
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1566
Nucleic Acid Atoms453
Solvent Atoms67
Heterogen Atoms2

Software

Software
Software NamePurpose
BESTdata collection
PHASERphasing
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling