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1.5 Angstrom crystal structure of a novel cobalamin-binding protein from Desulfitobacterium hafniense DCB-2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277.15 0.1 M MMT buffer, 25 % w/v PEG 1500, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 2.87 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.99 α = 90 b = 69.99 β = 90 c = 91.68 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 PIXEL PSI PILATUS 6M 2012-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.95 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 32.7 99 78874 75677 1.5 1.5
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 (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 1.5 32.69 78874 75677 3997 99.05 0.14971 0.14728 0.1571 0.1941 0.1996 RANDOM 27.258
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] 0.03 0.03 0.03 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.287 r_sphericity_free 22.138 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 13.485 r_sphericity_bonded 12.053 r_rigid_bond_restr 7.088 r_dihedral_angle_1_deg 6.091 r_angle_refined_deg 2.14 r_angle_other_deg 1.018 r_chiral_restr 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.287 r_sphericity_free 22.138 r_dihedral_angle_4_deg 15.345 r_dihedral_angle_3_deg 13.485 r_sphericity_bonded 12.053 r_rigid_bond_restr 7.088 r_dihedral_angle_1_deg 6.091 r_angle_refined_deg 2.14 r_angle_other_deg 1.018 r_chiral_restr 0.14 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3065 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 182
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement xia2 data reduction xia2 data scaling