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Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GP0 Homology models of D7, 8, 9, 10, Crystal structure of D11 (1GP0)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M MES pH 6.5, 1.6 M MgSO4, 10 mM mannose 6-phosphate
Crystal Properties Matthews coefficient Solvent content 3.75 67.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.204 α = 90 b = 139.204 β = 90 c = 234.682 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS EIGER2 XE 16M 2013-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.05811 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.47 89.72 98.55 0.997 6.03 14.5 30224
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.47 3.59 98.43 0.127 0.84 14.9
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Homology models of D7, 8, 9, 10, Crystal structure of D11 (1GP0) 3.47 89.72 30215 1493 98.55 0.2607 0.2696 0.3 0.2962 RANDOM 197.426
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] -0.15 -0.15 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_long_range_B_refined 25.876 r_long_range_B_other 25.876 r_scangle_other 16.286 r_dihedral_angle_3_deg 16.221 r_dihedral_angle_4_deg 15.811 r_mcangle_it 15.288 r_mcangle_other 15.288 r_scbond_it 10.345 r_scbond_other 10.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_long_range_B_refined 25.876 r_long_range_B_other 25.876 r_scangle_other 16.286 r_dihedral_angle_3_deg 16.221 r_dihedral_angle_4_deg 15.811 r_mcangle_it 15.288 r_mcangle_other 15.288 r_scbond_it 10.345 r_scbond_other 10.344 r_mcbond_it 9.748 r_mcbond_other 9.739 r_dihedral_angle_1_deg 8.862 r_angle_refined_deg 1.564 r_angle_other_deg 1.242 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10358 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 191
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing Coot model building