☰ Navigation Tabs
Structure of Cobalamin-complexed Bovine Transcobalamin in Monoclinic Crystal Form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other UNREFINED PARTIAL MODEL FROM PHASING WITH SHARP V2.0 USING SINGLE-WAVELENGTH ANOMALOUS DISPERSION DATA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 293 28% PEG 8000, 0.2M magnesium acetate, 20% 2-methyl-2,4-pentadiol, 0.1M TRIS, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.50
Crystal Properties Matthews coefficient Solvent content 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.826 α = 90 b = 100.664 β = 97.16 c = 99.143 γ = 90
Symmetry Space Group P 1 21 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 2002-12-13 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 2 18 96.8 0.097 0.097 12 3.5 121830 25.8
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 2 2.07 93.3 0.522 0.522 2.2 3.2
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 UNREFINED PARTIAL MODEL FROM PHASING WITH SHARP V2.0 USING SINGLE-WAVELENGTH ANOMALOUS DISPERSION DATA 2 18 116949 116949 4895 96.8 0.243 0.241 0.2521 0.28 0.2832 RANDOM 32.24
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] 0.79 0.27 -1.06 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.024 r_dihedral_angle_4_deg 23.697 r_dihedral_angle_3_deg 20.727 r_dihedral_angle_1_deg 6.996 r_scangle_it 3.192 r_scbond_it 1.953 r_mcangle_it 1.489 r_angle_refined_deg 1.355 r_mcbond_it 0.789 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.024 r_dihedral_angle_4_deg 23.697 r_dihedral_angle_3_deg 20.727 r_dihedral_angle_1_deg 6.996 r_scangle_it 3.192 r_scbond_it 1.953 r_mcangle_it 1.489 r_angle_refined_deg 1.355 r_mcbond_it 0.789 r_nbtor_refined 0.299 r_symmetry_vdw_refined 0.259 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 13016 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 368
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing