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Endo-glycoceramidase II from Rhodococcus sp.
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 2.24 45.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.75 α = 90 b = 92.941 β = 98.55 c = 94.545 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 100 IMAGE PLATE MAR scanner 345 mm plate 2005-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.6 30.979 99.2 0.053 0.053 9.5 6.4 119859 19.957
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) 1.6 1.69 98.2 0.335 0.335 2.2 6.4 17253
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 SAD THROUGHOUT 1.6 29.57 119829 6081 99.1 0.183 0.181 0.186 0.204 0.209 RANDOM 13.701
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] 0.93 -0.36 0.22 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.44 r_dihedral_angle_3_deg 11.774 r_dihedral_angle_4_deg 10.171 r_dihedral_angle_1_deg 5.717 r_scangle_it 1.659 r_angle_refined_deg 1.059 r_scbond_it 1.057 r_angle_other_deg 0.846 r_mcangle_it 0.747 r_mcbond_it 0.413
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.44 r_dihedral_angle_3_deg 11.774 r_dihedral_angle_4_deg 10.171 r_dihedral_angle_1_deg 5.717 r_scangle_it 1.659 r_angle_refined_deg 1.059 r_scbond_it 1.057 r_angle_other_deg 0.846 r_mcangle_it 0.747 r_mcbond_it 0.413 r_symmetry_vdw_other 0.257 r_nbd_refined 0.196 r_nbd_other 0.19 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.135 r_mcbond_other 0.132 r_metal_ion_refined 0.094 r_xyhbond_nbd_refined 0.091 r_symmetry_hbond_refined 0.084 r_nbtor_other 0.082 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6877 Nucleic Acid Atoms Solvent Atoms 880 Heterogen Atoms 20
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling SOLVE phasing