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Crystallographic analysis of upper axial ligand substitutions in cobalamin bound to transcobalamin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BBC PDB ENTRY 2BBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 PROTEIN AT 0.5 MM IN 1 M NACL, 0.1 M TRIS, PH 7.5 CRYSTALLIZED FROM 28% PEG 8000, 0.2 M MAGNESIUM ACETATE, 0.1 M TRIS PH 8.5, 20% 2-METHYL-2, 4-PENTADIOL, 15 MM KCN
Crystal Properties Matthews coefficient Solvent content 4.1 69.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.83 α = 90 b = 100.83 β = 90 c = 130.215 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 2007-04-04 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) 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 2.7 20.7 99.3 0.12 9.7 3.1 21370
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 2.7 2.85 99.9 0.75 1.7 3.1
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BBC 2.73 20.7 20574 857 99.3 0.213 0.211 0.2027 0.251 0.2428 RANDOM 43.4
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] 0.433 0.216 0.433 -0.649
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_dihedral_angle_4_deg 20.715 r_dihedral_angle_3_deg 17.011 r_dihedral_angle_1_deg 5.771 r_scangle_it 2.275 r_scbond_it 1.319 r_angle_refined_deg 1.308 r_mcangle_it 1.181 r_mcbond_it 0.661 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.867 r_dihedral_angle_4_deg 20.715 r_dihedral_angle_3_deg 17.011 r_dihedral_angle_1_deg 5.771 r_scangle_it 2.275 r_scbond_it 1.319 r_angle_refined_deg 1.308 r_mcangle_it 1.181 r_mcbond_it 0.661 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.255 r_symmetry_hbond_refined 0.225 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.082 r_bond_refined_d 0.01 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_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 3178 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling REFMAC phasing