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Human cation-independent mannose 6-phosphate/ IGF2 receptor domain 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Domain 10 from the crystal structure of cation-independent mannose 6-phosphate receptor domains 9-10 (separate deposition)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 1.5 M Ammonium sulphate, 0.1 M Tris pH 8.5, 12 % glycerol
Crystal Properties Matthews coefficient Solvent content 3.12 60.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.555 α = 90 b = 45.537 β = 116.36 c = 70.275 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 80 PIXEL DECTRIS PILATUS3 6M 2020-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 2.56 36.02 98.98 0.975 5.59 4.7 12121 40.52
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 2.56 2.65 95.82 0.686 1.97 4.6
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Domain 10 from the crystal structure of cation-independent mannose 6-phosphate receptor domains 9-10 (separate deposition) 2.56 36.02 12116 98.98 0.2234 0.2223 0.2508 0.2494
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2095 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 4
Software Software Software Name Purpose PHENIX refinement xia2 data reduction DIALS data scaling PHASER phasing Coot model building