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The structure of a putative RNA methyltransferase of the TrmH family from Porphyromonas gingivalis.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 291 0.8M NaH2PO4, 1.2M K2HPO4, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.921 α = 90 b = 107.119 β = 90 c = 120.352 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2005-07-24 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97951, 0.97962 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.85 37.1 98.3 11.4 3 23206 23206 -3 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 89.2 2.35 4.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.85 37.1 23206 22012 1193 98.33 0.19126 0.18892 0.1873 0.2347 0.2316 RANDOM 34.802
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] 0.9 -0.04 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.463 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_4_deg 12.033 r_dihedral_angle_1_deg 5.269 r_scangle_it 3.317 r_scbond_it 2.294 r_angle_refined_deg 1.415 r_mcangle_it 1.366 r_mcbond_it 0.996 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.463 r_dihedral_angle_3_deg 15.601 r_dihedral_angle_4_deg 12.033 r_dihedral_angle_1_deg 5.269 r_scangle_it 3.317 r_scbond_it 2.294 r_angle_refined_deg 1.415 r_mcangle_it 1.366 r_mcbond_it 0.996 r_nbtor_refined 0.311 r_symmetry_hbond_refined 0.232 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 1933 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building