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The crystal structure at 1.7 A resolution of CobE, a protein from the cobalamin (vitamin B12) biosynthetic pathway
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1M MES PH6.9, 2M AMMONIUM SULPHATE, 5% DIOXANE
Crystal Properties Matthews coefficient Solvent content 1.9 35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.729 α = 90 b = 41.271 β = 90 c = 87.94 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MARRESEARCH M SINGLE WAVELENGTH 2 1 x-ray CCD ADSC CCD M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1 2 SYNCHROTRON ESRF BEAMLINE BM14 0.95372, 0.97925, 0.97944 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 45 97.3 0.05 30.4 12.5 13347 2
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 1.76 96 0.49 7.1 11.8
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 MAD THROUGHOUT NONE 1.7 30.1 12361 619 97.1 0.202 0.199 0.2036 0.25 0.2563 RANDOM 20.44
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] -0.86 0.69 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.253 r_dihedral_angle_4_deg 21.899 r_dihedral_angle_3_deg 18.159 r_dihedral_angle_1_deg 7.099 r_scangle_it 3.797 r_scbond_it 2.393 r_mcangle_it 1.814 r_angle_refined_deg 1.69 r_mcbond_it 1.056 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.253 r_dihedral_angle_4_deg 21.899 r_dihedral_angle_3_deg 18.159 r_dihedral_angle_1_deg 7.099 r_scangle_it 3.797 r_scbond_it 2.393 r_mcangle_it 1.814 r_angle_refined_deg 1.69 r_mcbond_it 1.056 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.251 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.162 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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_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 1053 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing