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The crystal structure of probable ornithine cyclodeaminase from Bordetella pertussis Tohama I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 297 2.5M NaCl,
0.1M imidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.59 52.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.405 α = 90 b = 50.923 β = 100.98 c = 106.999 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315 mirror 2008-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
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 1.7 39.5 99.5 0.092 24.7 4.5 73662 73662
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 1.7 1.73 97.7 0.765 1.64 4 3592
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.7 39.41 69889 69889 3714 99.36 0.17993 0.17993 0.1782 0.1928 0.21189 0.226 RANDOM 17.378
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 -0.03 0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.944 r_dihedral_angle_4_deg 19.209 r_dihedral_angle_3_deg 15.883 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.177 r_scbond_it 2.583 r_mcangle_it 1.505 r_angle_refined_deg 1.488 r_mcbond_it 0.867 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.944 r_dihedral_angle_4_deg 19.209 r_dihedral_angle_3_deg 15.883 r_dihedral_angle_1_deg 5.9 r_scangle_it 4.177 r_scbond_it 2.583 r_mcangle_it 1.505 r_angle_refined_deg 1.488 r_mcbond_it 0.867 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4556 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 34
Software Software Software Name Purpose SBC-Collect data collection SHELXD phasing MLPHARE phasing DM model building ARP model building WARP model building HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing