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Crystal Structure of the vitamin B12 biosynthetic cobaltochelatase, CbiXS, from Archaeoglobus fulgidus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TJN PDB ENTRY 1TJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 298 1.9M ammonium phosphate pH6.8, 4% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.81 56.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.721 α = 90 b = 62.721 β = 90 c = 150.609 γ = 120
Symmetry Space Group P 31 2 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 210 2004-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.019943 ALS 8.3.1
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 2.5 60 69 0.06 12.8 12517 8637 1.9 1.9
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 2.5 2.59 48.9 0.265 1.9
Refinement Statistics Diffraction ID Structure Solution Method Starting model 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 MOLECULAR REPLACEMENT PDB ENTRY 1TJN 2.55 54.3 11184 7925 409 70.9 0.215 0.215 0.212 0.1958 0.267 0.1798 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.832 r_dihedral_angle_3_deg 19.095 r_scangle_it 17.282 r_dihedral_angle_4_deg 13.657 r_scbond_it 12.934 r_mcangle_it 9.358 r_mcbond_it 6.79 r_dihedral_angle_1_deg 6.602 r_angle_refined_deg 1.479 r_symmetry_hbond_refined 0.414
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.832 r_dihedral_angle_3_deg 19.095 r_scangle_it 17.282 r_dihedral_angle_4_deg 13.657 r_scbond_it 12.934 r_mcangle_it 9.358 r_mcbond_it 6.79 r_dihedral_angle_1_deg 6.602 r_angle_refined_deg 1.479 r_symmetry_hbond_refined 0.414 r_symmetry_vdw_refined 0.364 r_nbtor_refined 0.318 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.186 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 2020 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 38
Software Software Software Name Purpose Blu-Ice data collection HKL-2000 data reduction MOLREP phasing REFMAC refinement HKL-2000 data scaling