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Co-crystal structure of Mouse Nicotinamide N-methyltransferase (NNMT) with small molecule analog of Nicotinamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ROD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.35M Sodium thiocynate, 20% PEG 3350, with 0.01M TMAO as additive
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.356 α = 90 b = 71.622 β = 90 c = 157.408 γ = 90
Symmetry Space Group P 21 21 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 315r 2016-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 Australian Synchrotron MX2
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 1.99 47.36 99.6 14.2 9.5 37822
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 0.52 0.182
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 3ROD 1.99 47.36 35850 1890 99.59 0.21157 0.21017 0.2104 0.23825 0.2375 RANDOM 19.797
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] -0.16 0.81 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.589 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 5.509 r_scangle_it 2.05 r_scbond_it 1.216 r_angle_refined_deg 1.153 r_mcangle_it 0.913 r_mcbond_it 0.517 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.589 r_dihedral_angle_4_deg 17.992 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 5.509 r_scangle_it 2.05 r_scbond_it 1.216 r_angle_refined_deg 1.153 r_mcangle_it 0.913 r_mcbond_it 0.517 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.184 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other 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 Atoms Number Protein Atoms 3982 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing