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Crystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CCU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 PEG800 SODIUM HYDROXIDE AMMONIUM
CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.4 48.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.283 α = 90 b = 48.921 β = 113.95 c = 120.227 γ = 90
Symmetry Space Group C 1 2 1
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 315 2015-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 2.15 50 99.2 0.118 13.25 4.2 55310
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 0.485 0.269
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 5CCU 2.15 50 51963 2776 97.8 0.169 0.167 0.1769 0.203 0.2096 RANDOM 24.94
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] -0.18 -0.05 0.29 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.348 r_dihedral_angle_4_deg 22.246 r_dihedral_angle_3_deg 13.822 r_dihedral_angle_1_deg 6.223 r_long_range_B_refined 4.334 r_long_range_B_other 4.333 r_scangle_other 3.017 r_mcangle_it 1.985 r_mcangle_other 1.984 r_scbond_it 1.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.348 r_dihedral_angle_4_deg 22.246 r_dihedral_angle_3_deg 13.822 r_dihedral_angle_1_deg 6.223 r_long_range_B_refined 4.334 r_long_range_B_other 4.333 r_scangle_other 3.017 r_mcangle_it 1.985 r_mcangle_other 1.984 r_scbond_it 1.863 r_scbond_other 1.863 r_angle_refined_deg 1.458 r_angle_other_deg 1.333 r_mcbond_it 1.245 r_mcbond_other 1.245 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_bond_other_d 0.006 r_gen_planes_refined 0.006 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 6801 Nucleic Acid Atoms Solvent Atoms 380 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing