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Partially deglycosylated glucoceramidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGS PDB ENTRY 1OGS MOLECULE A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 1M BIS-TRIS PH 5.5, 2M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.626 α = 90 b = 280.821 β = 90 c = 91.064 γ = 90
Symmetry Space Group C 2 2 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 ADSC CORPORATION 2005-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.6 29.67 98.7 0.11 13.75 7.3 30978 29.58
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 2.6 2.9 98.6 0.27 5.3 7.5
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 1OGS MOLECULE A 2.9 29.67 29797 1539 100 0.218 0.215 0.2152 0.273 0.27 RANDOM 33.66
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 18.915 r_dihedral_angle_1_deg 6.627 r_scangle_it 1.965 r_angle_refined_deg 1.59 r_mcangle_it 1.256 r_scbond_it 1.178 r_mcbond_it 0.727 r_nbtor_refined 0.332
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.326 r_dihedral_angle_4_deg 21.704 r_dihedral_angle_3_deg 18.915 r_dihedral_angle_1_deg 6.627 r_scangle_it 1.965 r_angle_refined_deg 1.59 r_mcangle_it 1.256 r_scbond_it 1.178 r_mcbond_it 0.727 r_nbtor_refined 0.332 r_symmetry_vdw_refined 0.278 r_symmetry_hbond_refined 0.278 r_nbd_refined 0.242 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.122 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 7801 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing