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The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor str. N16961
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 10mM Sodium citrate, 33% PEG 6000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.56 51.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.305 α = 90 b = 61.456 β = 90 c = 210.343 γ = 90
Symmetry Space Group C 2 2 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 315 mirrors 2008-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 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 2 105.41 99.54 0.097 14.72 9.5 26026 25897 2 2 22
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 2 2.052 100 0.661 1.9 9.7 2035
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 SAD THROUGHOUT 2 105.41 1.9 26026 25897 1368 99.54 0.20506 0.20204 0.2168 0.26234 0.2721 RANDOM 21.81
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] -0.35 0.4 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.085 r_dihedral_angle_4_deg 17.116 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.149 r_scangle_it 5.417 r_scbond_it 3.328 r_angle_refined_deg 1.922 r_mcangle_it 1.904 r_angle_other_deg 1.116 r_mcbond_it 1.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.085 r_dihedral_angle_4_deg 17.116 r_dihedral_angle_3_deg 15.286 r_dihedral_angle_1_deg 6.149 r_scangle_it 5.417 r_scbond_it 3.328 r_angle_refined_deg 1.922 r_mcangle_it 1.904 r_angle_other_deg 1.116 r_mcbond_it 1.102 r_mcbond_other 0.347 r_chiral_restr 0.15 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 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 2620 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 2
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling