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Structure and Catalytic Mechanism of Bordetella bronchiseptica nicF
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBA PDB entry 1NBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 0.1 M cacodylic acid, 0.2 M ammonium acetate, 30% PEG-8000, 10 mg/mL protein in 10% glycerol, pH 6.5, 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 2010-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54
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 2.4 12.01 91.7 0.087 9.78 2.2 68504 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 2.4 2.52 67.5 0.271 2.9 1.2
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 1NBA 2.4 12.01 68504 1400 98.09 0.24201 0.24058 0.2413 0.31097 0.3084 RANDOM 14.58
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] 0.02 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.139 r_dihedral_angle_3_deg 17.139 r_dihedral_angle_4_deg 16.031 r_dihedral_angle_1_deg 11.133 r_scangle_it 2.279 r_angle_refined_deg 1.563 r_scbond_it 1.45 r_angle_other_deg 1.104 r_mcangle_it 0.859 r_mcbond_it 0.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.139 r_dihedral_angle_3_deg 17.139 r_dihedral_angle_4_deg 16.031 r_dihedral_angle_1_deg 11.133 r_scangle_it 2.279 r_angle_refined_deg 1.563 r_scbond_it 1.45 r_angle_other_deg 1.104 r_mcangle_it 0.859 r_mcbond_it 0.498 r_mcbond_other 0.099 r_chiral_restr 0.086 r_bond_refined_d 0.015 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 11740 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms
Software Software Software Name Purpose CrysalisPro data collection PHASER phasing REFMAC refinement CrysalisPro data reduction CrysalisPro data scaling