☰ Navigation Tabs
Cobalt chelatase CbiK (periplasmic) from Desulvobrio vulgaris Hildenborough (co-crystallised with cobalt and SHC)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XVZ PDB ENTRY 2XVZ
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 1.8UL OF CRYSTALLIZATION SOLUTION AND 0.2UL OF 2MM SIROHYDROCHLORIN AND 0.2UL OF COBALT CHLORIDE IN AEROBIC CONDITIONS.
Crystal Properties Matthews coefficient Solvent content 3.6 65.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.81 α = 90 b = 120.81 β = 90 c = 119.71 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 MARRESEARCH COLLIMATING RHODIUM COATED MIRROR (BEFORE MONOCHROMATOR) AND FOCUSSING TOROIDAL RHODIUM COATED MIRROR (AFTER MONOCHROMATOR) 2007-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 49.24 96.7 0.04 20.8 5.4 46830 30.5
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 1.7 1.81 84.4 0.46 2.9 4.4
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 2XVZ 1.7 85.44 44493 2379 96.79 0.17296 0.17215 0.171 0.18779 0.1866 RANDOM 25.875
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] -0.43 -0.43 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 18.116 r_dihedral_angle_3_deg 12.76 r_dihedral_angle_1_deg 5.026 r_scangle_it 4.83 r_scbond_it 3.036 r_mcangle_it 1.915 r_angle_refined_deg 1.762 r_mcbond_it 1.088 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.72 r_dihedral_angle_4_deg 18.116 r_dihedral_angle_3_deg 12.76 r_dihedral_angle_1_deg 5.026 r_scangle_it 4.83 r_scbond_it 3.036 r_mcangle_it 1.915 r_angle_refined_deg 1.762 r_mcbond_it 1.088 r_chiral_restr 0.123 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 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 238 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling PHASER phasing