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The Crystal structure of the Carbohydrate recognition domain of the glycoprotein sorting receptor p58/ERGIC-53 reveals a novel metal binding site and conformational changes associated with calcium ion binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 PEG8000, Calcium Chloride, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.351 α = 91.05 b = 81.068 β = 94.14 c = 82.306 γ = 94.99
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 ADSC QUANTUM 4 2002-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 10 95.7 0.126 0.096 13 2.3 98470 42617 1 1 45.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.53 95.7 0.43 0.33 1.7 2.3 6205
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1gv9 2.4 10 0.005 0.005 42617 41040 1071 94.55 0.223 0.22297 0.2225 0.3002 0.24063 0.3041 RANDOM 21.012
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] 1.56 -2.51 -1.35 -3.33 0.89 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.256 r_scangle_it 2.33 r_scbond_it 1.457 r_angle_refined_deg 1.225 r_mcangle_it 0.944 r_mcbond_it 0.496 r_symmetry_vdw_refined 0.425 r_symmetry_hbond_refined 0.313 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.256 r_scangle_it 2.33 r_scbond_it 1.457 r_angle_refined_deg 1.225 r_mcangle_it 0.944 r_mcbond_it 0.496 r_symmetry_vdw_refined 0.425 r_symmetry_hbond_refined 0.313 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.204 r_chiral_restr 0.089 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7592 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling AMoRE phasing