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Structure of Human Transcobalamin in complex with Cobalamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BB6 STRUCTURE OF BOVINE TRANSCOBALAMIN IN MONOCLINIC CRYSTAL FORM (PDB 2BB6).
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.6 293 20% PEG 4000, 18% ethanol, 0.2M TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 7.60
Crystal Properties Matthews coefficient Solvent content 3.23 61.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.127 α = 90 b = 145.497 β = 90 c = 165.043 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 CCD MARRESEARCH 2001-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.2 29.24 96.5 0.142 0.142 4.5 2.3 19417
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.37 95.5 0.388 0.388 1.9 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 STRUCTURE OF BOVINE TRANSCOBALAMIN IN MONOCLINIC CRYSTAL FORM (PDB 2BB6). 3.2 20 19334 19334 997 95.6 0.258 0.257 0.2518 0.288 0.2762 RANDOM 40.46
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] -2.42 4.91 -2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.095 r_dihedral_angle_4_deg 22.701 r_dihedral_angle_3_deg 18.765 r_dihedral_angle_1_deg 4.611 r_angle_refined_deg 1.094 r_scangle_it 0.984 r_mcangle_it 0.721 r_scbond_it 0.569 r_mcbond_it 0.392 r_symmetry_hbond_refined 0.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.095 r_dihedral_angle_4_deg 22.701 r_dihedral_angle_3_deg 18.765 r_dihedral_angle_1_deg 4.611 r_angle_refined_deg 1.094 r_scangle_it 0.984 r_mcangle_it 0.721 r_scbond_it 0.569 r_mcbond_it 0.392 r_symmetry_hbond_refined 0.357 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.25 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.002 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 6406 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 182
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling AMoRE phasing