☰ Navigation Tabs
Crystal structure of human methylmalonyl-CoA mutase in complex with adenosylcobalamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BIC PDB ENTRY 3BIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 30% PEG3350, 0.1 M BIS-TRIS PH 5.5, 0.3 M NH4-SULPHATE
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.36 α = 90 b = 137.72 β = 90 c = 198.4 γ = 90
Symmetry Space Group C 2 2 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 CCD ADSC CCD 2010-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.95 47.8 98.1 0.08 13.2 3.8 59702 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 1.95 2.06 97.6 0.52 2.5 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 3BIC 1.95 99.2 2 55480 2953 97.86 0.16007 0.158 0.1619 0.19902 0.2015 RANDOM 16.024
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] 1.18 -1.3 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 14.802 r_dihedral_angle_3_deg 12.609 r_dihedral_angle_1_deg 6.312 r_angle_refined_deg 1.591 r_angle_other_deg 0.803 r_chiral_restr 0.127 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.909 r_dihedral_angle_4_deg 14.802 r_dihedral_angle_3_deg 12.609 r_dihedral_angle_1_deg 6.312 r_angle_refined_deg 1.591 r_angle_other_deg 0.803 r_chiral_restr 0.127 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 5435 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 165
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing