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Acinetobacter baumanii nicotinamidase pyrazinamidease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IM5 PDB ENTRY 1IM5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 2.0 M AMMONIUM SULPHATE, 200 MM SODIUM CACODYLATE, PH 5.5, 200 MM LITHIUM CHLORIDE AND 20% GLYCEROL.
Crystal Properties Matthews coefficient Solvent content 2.2 44.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.64 α = 113.19 b = 46.89 β = 88.25 c = 59.48 γ = 115.61
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.65 28.4 88.6 0.08 12.2 3.4 47549
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 1.65 1.69 75.4 0.49 3.25 3.4
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 1IM5 1.65 28.4 45170 2378 100 0.182 0.179 0.1929 0.235 0.2483 RANDOM 20.03
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] 4.23 1.88 0.42 -0.77 -0.52 -2.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 15.286 r_dihedral_angle_3_deg 14.354 r_dihedral_angle_1_deg 6.731 r_scangle_it 5.069 r_mcangle_it 4.096 r_scbond_it 3.762 r_mcbond_it 3.189 r_angle_refined_deg 1.914 r_mcbond_other 1.176
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.618 r_dihedral_angle_4_deg 15.286 r_dihedral_angle_3_deg 14.354 r_dihedral_angle_1_deg 6.731 r_scangle_it 5.069 r_mcangle_it 4.096 r_scbond_it 3.762 r_mcbond_it 3.189 r_angle_refined_deg 1.914 r_mcbond_other 1.176 r_angle_other_deg 1.053 r_chiral_restr 0.115 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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_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 3208 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing