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Structure and Catalytic Mechanism of the Vitamin B3 Degradative Enzyme Maleamate Amidohydrolase from Bordetalla bronchiseptica RB50
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBA PDB ENTRY 1NBA MODIFIED TO TARGET SEQUENCE USING PHYRE SERVER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.2 M ammonium acetate, 0.1 M sodium cacodylate, 30% PEG-8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.35 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.56 α = 90 b = 157.56 β = 90 c = 198.48 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD OXFORD RUBY CCD mirrors 2010-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.399 12.01 91.7 0.087 9.78 2.2 143682 131825 3 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.399 2.52 67.5 0.271 1.2 13186
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1NBA MODIFIED TO TARGET SEQUENCE USING PHYRE SERVER 2.399 12.01 143682 131825 1368 97.94 0.12796 0.12704 0.1249 0.17252 0.1664 RANDOM 14.739
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] -0.63 -0.63 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.656 r_dihedral_angle_4_deg 16.457 r_dihedral_angle_3_deg 16.308 r_dihedral_angle_1_deg 10.077 r_scangle_it 3.047 r_scbond_it 1.891 r_angle_refined_deg 1.626 r_mcangle_it 1.136 r_angle_other_deg 1.133 r_mcbond_it 0.651
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.656 r_dihedral_angle_4_deg 16.457 r_dihedral_angle_3_deg 16.308 r_dihedral_angle_1_deg 10.077 r_scangle_it 3.047 r_scbond_it 1.891 r_angle_refined_deg 1.626 r_mcangle_it 1.136 r_angle_other_deg 1.133 r_mcbond_it 0.651 r_mcbond_other 0.137 r_chiral_restr 0.097 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11822 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms 64
Software Software Software Name Purpose CrysalisPro data collection PHASER phasing REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling