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Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 294 20% (w/v) PEG 3350; 0.175 M NaCl; 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.801 α = 90 b = 61.984 β = 112.25 c = 102.846 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 2006-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0000 ALS 8.2.2
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 1.1 31.734 93.8 0.054 0.054 9.2 4.2 171712 7.094
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) 1 1.1 1.16 89.9 0.463 0.463 1.5 4.2 23927
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.1 46.23 171710 8690 93.86 0.122 0.121 0.1306 0.139 0.1471 RANDOM 7.65
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] 0.08 0.03 -0.19 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.712 r_dihedral_angle_4_deg 12.93 r_dihedral_angle_3_deg 11.374 r_sphericity_free 6.678 r_dihedral_angle_1_deg 6.178 r_sphericity_bonded 3.68 r_scangle_it 2.942 r_scbond_it 2.206 r_mcangle_it 1.742 r_angle_refined_deg 1.468
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.712 r_dihedral_angle_4_deg 12.93 r_dihedral_angle_3_deg 11.374 r_sphericity_free 6.678 r_dihedral_angle_1_deg 6.178 r_sphericity_bonded 3.68 r_scangle_it 2.942 r_scbond_it 2.206 r_mcangle_it 1.742 r_angle_refined_deg 1.468 r_mcbond_it 1.159 r_rigid_bond_restr 0.975 r_angle_other_deg 0.955 r_mcbond_other 0.596 r_symmetry_vdw_refined 0.348 r_symmetry_vdw_other 0.292 r_nbd_refined 0.212 r_nbd_other 0.207 r_nbtor_refined 0.182 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.131 r_metal_ion_refined 0.13 r_chiral_restr 0.09 r_nbtor_other 0.09 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3452 Nucleic Acid Atoms Solvent Atoms 598 Heterogen Atoms 73
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling MOLREP phasing