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Crystal structure of a C.elegans B12-trafficking protein CblC, a human MMACHC homologue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SBZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 21.5% PEG 3350, 40 mM Spermidine-HCl, 0.2 M (NH4)2tartarate
Crystal Properties Matthews coefficient Solvent content 2.61 52.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.008 α = 90 b = 66.089 β = 90 c = 92.826 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 MARMOSAIC 300 mm CCD K-B pair of biomorph mirrors for vertical and horizontal focusing 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03325 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) CC (Half) 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 1.35 53.84 92.9 0.054 0.062 0.029 0.997 15 3.8 66799 12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.37 58.7 0.573 0.722 0.435 0.618 1.9 2.3
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 3SBZ 1.35 53.84 63476 3285 92.28 0.13361 0.13209 0.1333 0.16303 0.1648 RANDOM 18.25
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] -0.92 1.79 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.461 r_sphericity_bonded 13.967 r_dihedral_angle_4_deg 12.944 r_dihedral_angle_3_deg 11.867 r_dihedral_angle_1_deg 5.93 r_long_range_B_refined 3.992 r_long_range_B_other 3.615 r_scangle_other 3.447 r_scbond_it 2.902 r_scbond_other 2.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.461 r_sphericity_bonded 13.967 r_dihedral_angle_4_deg 12.944 r_dihedral_angle_3_deg 11.867 r_dihedral_angle_1_deg 5.93 r_long_range_B_refined 3.992 r_long_range_B_other 3.615 r_scangle_other 3.447 r_scbond_it 2.902 r_scbond_other 2.902 r_mcangle_it 2.713 r_mcangle_other 2.713 r_rigid_bond_restr 2.233 r_mcbond_other 2.195 r_mcbond_it 2.194 r_angle_refined_deg 2.013 r_angle_other_deg 0.736 r_chiral_restr 0.541 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_scangle_it r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2184 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing