3L8U

Crystal structure of SMU.1707c, a putative rRNA methyltransferase from streptococcus mutans UA159


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3E5YPDB ENTRY 3E5Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72931.5M (NH4)2SO4, 0.1M Bis-tris pH7.0, 0.7% beta-OG , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8356.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.277α = 90
b = 82.277β = 90
c = 70.992γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4r2009-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6A1.0Photon FactoryBL-6A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125099.331965317721

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 3E5Y235.630118160499.260.207630.206030.23896RANDOM41.124
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]
-0.37-0.370.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.219
r_dihedral_angle_4_deg22.211
r_dihedral_angle_3_deg16.07
r_dihedral_angle_1_deg5.709
r_scangle_it3.834
r_scbond_it2.669
r_mcangle_it1.746
r_angle_refined_deg1.633
r_mcbond_it1.157
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.219
r_dihedral_angle_4_deg22.211
r_dihedral_angle_3_deg16.07
r_dihedral_angle_1_deg5.709
r_scangle_it3.834
r_scbond_it2.669
r_mcangle_it1.746
r_angle_refined_deg1.633
r_mcbond_it1.157
r_nbtor_refined0.304
r_chiral_restr0.264
r_nbd_refined0.214
r_symmetry_vdw_refined0.213
r_symmetry_hbond_refined0.179
r_xyhbond_nbd_refined0.154
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2464
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling