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Structure of the O-methyltransferase NovP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VID PDB ENTRY 1VID
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 2 M AMMONIUM SULPHATE, 100 MM HEPES BUFFER PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.19 43.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.813 α = 90 b = 46.038 β = 104.97 c = 61.22 γ = 90
Symmetry Space Group P 1 2 1
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 MARRESEARCH 2005-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.4 36.3 98.8 0.06 18.1 3.4 54638 -3 17.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 89.5 0.16 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1VID 1.4 34.1 54636 2795 98.8 0.146 0.145 0.1511 0.163 0.1683 RANDOM 13.38
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] 0.223 -0.005 0.132 -0.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.793 r_dihedral_angle_4_deg 16.041 r_dihedral_angle_3_deg 11.551 r_dihedral_angle_1_deg 5.83 r_sphericity_free 5.508 r_scangle_it 5.041 r_scbond_it 3.447 r_sphericity_bonded 3.446 r_mcangle_it 2.301 r_angle_refined_deg 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.793 r_dihedral_angle_4_deg 16.041 r_dihedral_angle_3_deg 11.551 r_dihedral_angle_1_deg 5.83 r_sphericity_free 5.508 r_scangle_it 5.041 r_scbond_it 3.447 r_sphericity_bonded 3.446 r_mcangle_it 2.301 r_angle_refined_deg 1.54 r_rigid_bond_restr 1.49 r_mcbond_it 1.391 r_symmetry_vdw_refined 0.635 r_mcbond_other 0.585 r_symmetry_vdw_other 0.497 r_nbd_refined 0.394 r_symmetry_hbond_refined 0.294 r_chiral_restr 0.259 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.157 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1934 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling