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Structure of Cobalamin-complexed Bovine Transcobalamin in trigonal crystal form
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 VAPOR DIFFUSION, HANGING DROP 8.5 293 28% PEG 8000, 0.2M magnesium acetate, 20% 2-methyl-2,4-pentadiol, 0.1M TRIS 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.97 69.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.57 α = 90 b = 99.57 β = 90 c = 128.631 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 MARRESEARCH 2004-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 2.4 50 99 0.054 24.3 3.7 29190 29142 55.7
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 2.4 2.49 98.7 98.7 0.607 2.1 3.5 2875
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 (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 THROUGHOUT Structure of Bovine Transcobalamin in monoclinic crystal form (PDB 2BB6). 2.4 20 27934 27934 1192 99.34 0.205 0.205 0.204 0.215 0.24 0.2458 RANDOM 54.845
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] 0.64 0.32 0.64 -0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.804 r_dihedral_angle_4_deg 21.175 r_dihedral_angle_3_deg 19.003 r_dihedral_angle_1_deg 6.987 r_scangle_it 3.59 r_scbond_it 2.239 r_mcangle_it 1.768 r_angle_refined_deg 1.543 r_mcbond_it 0.95 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.804 r_dihedral_angle_4_deg 21.175 r_dihedral_angle_3_deg 19.003 r_dihedral_angle_1_deg 6.987 r_scangle_it 3.59 r_scbond_it 2.239 r_mcangle_it 1.768 r_angle_refined_deg 1.543 r_mcbond_it 0.95 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.29 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3254 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 94
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing