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Cobalt chelatase CbiK (periplasmatic) from Desulvobrio vulgaris Hildenborough (Native)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other MODEL OBTAINED WITH THE PROTEIN CO- CRYSTALLIZED WITH COBALT.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 CRYSTALLIZATION SOLUTION: 100MM TRIS-HCL PH8.5, 2M AMMONIUM SULFATE. THE DROP WAS MADE BY ADDING 1UL OF PROTEIN PLUS 2UL OF CRYSTALLIZATION SOLUTION.
Crystal Properties Matthews coefficient Solvent content 3.6 66.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.062 α = 90 b = 121.062 β = 90 c = 120.246 γ = 90
Symmetry Space Group I 4 2 2
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 MIRRORS 2007-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.9 42.8 99.9 0.08 7.6 28 35365 25.5
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 1.9 2 99.2 0.83 0.9 20.3
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 MODEL OBTAINED WITH THE PROTEIN CO- CRYSTALLIZED WITH COBALT. 1.9 85.6 33596 1768 99.86 0.17477 0.17351 0.173 0.19875 0.1989 RANDOM 29.552
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] -0.3 -0.3 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.235 r_dihedral_angle_4_deg 19.06 r_dihedral_angle_3_deg 13.18 r_dihedral_angle_1_deg 5.154 r_scangle_it 4.967 r_scbond_it 3.044 r_mcangle_it 2.075 r_angle_refined_deg 1.767 r_mcbond_it 1.145 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.235 r_dihedral_angle_4_deg 19.06 r_dihedral_angle_3_deg 13.18 r_dihedral_angle_1_deg 5.154 r_scangle_it 4.967 r_scbond_it 3.044 r_mcangle_it 2.075 r_angle_refined_deg 1.767 r_mcbond_it 1.145 r_chiral_restr 0.122 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 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_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 1979 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 133
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling PHASER phasing