3LL7

Crystal structure of putative methyltransferase PG_1098 from Porphyromonas gingivalis W83


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.1M HEPES, 10% PEG8000, 8% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7955.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.132α = 90
b = 78.485β = 104.65
c = 64.063γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97901APS19-ID

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
11.85099.90.99926.354722447195-321.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8399.70.6652.364.62387

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)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 DIFFRACTIONSADTHROUGHOUT1.8504712347123238199.760.182890.182890.18150.20863RANDOM16.297
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]
1.22-1.13-0.76-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.338
r_dihedral_angle_4_deg14.972
r_dihedral_angle_3_deg12.719
r_dihedral_angle_1_deg5.85
r_scangle_it3.584
r_scbond_it2.17
r_angle_refined_deg1.541
r_mcangle_it1.354
r_mcbond_it0.762
r_chiral_restr0.108
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.338
r_dihedral_angle_4_deg14.972
r_dihedral_angle_3_deg12.719
r_dihedral_angle_1_deg5.85
r_scangle_it3.584
r_scbond_it2.17
r_angle_refined_deg1.541
r_mcangle_it1.354
r_mcbond_it0.762
r_chiral_restr0.108
r_bond_refined_d0.014
r_gen_planes_refined0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3159
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms31

Software

Software
Software NamePurpose
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing