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Crystal structure of N-terminal truncated human B12-chaperone CblD (108-296)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CUZ PDB entry 5CUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20 % PEG3350, 0.1M Tris-HCl, pH 7.5, 0.2 M MgCl2, 0.1 M NaF
Crystal Properties Matthews coefficient Solvent content 2.3 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.638 α = 90 b = 67.111 β = 110.54 c = 66.219 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 MARMOSAIC 300 mm CCD 2012-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03299 APS 23-ID-B
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 1.9 50 98.1 0.079 13.1 3.2 30281
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 1.9 1.97 97 0.417 2.5 2.8
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 5CUZ 1.9 31.39 28735 1523 97.62 0.18811 0.18598 0.1872 0.22722 0.2289 RANDOM 26.348
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] 1.87 -0.78 0.32 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.892 r_dihedral_angle_4_deg 14.045 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 5.398 r_angle_refined_deg 1.392 r_angle_other_deg 0.781 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.892 r_dihedral_angle_4_deg 14.045 r_dihedral_angle_3_deg 13.468 r_dihedral_angle_1_deg 5.398 r_angle_refined_deg 1.392 r_angle_other_deg 0.781 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 2655 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing