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Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like imidazole complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSW PDB ENTRY 2OSW
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 45.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.752 α = 90 b = 93.246 β = 98.35 c = 94.432 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 CCD ADSC QUANTUM 315 2005-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9796 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 1.8 66 100 0.069 0.069 8.1 7.3 85295 19.018
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 1.8 1.9 100 0.39 0.39 2 7.2 12409
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 2OSW 1.8 53.15 85266 4295 99.99 0.175 0.174 0.1783 0.205 0.2086 RANDOM 13.838
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] 1.04 -0.04 0.54 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.54 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_4_deg 11.081 r_dihedral_angle_1_deg 5.88 r_scangle_it 1.701 r_angle_refined_deg 1.111 r_scbond_it 1.103 r_angle_other_deg 0.869 r_mcangle_it 0.815 r_mcbond_it 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.54 r_dihedral_angle_3_deg 11.711 r_dihedral_angle_4_deg 11.081 r_dihedral_angle_1_deg 5.88 r_scangle_it 1.701 r_angle_refined_deg 1.111 r_scbond_it 1.103 r_angle_other_deg 0.869 r_mcangle_it 0.815 r_mcbond_it 0.46 r_symmetry_vdw_other 0.22 r_nbd_refined 0.194 r_nbd_other 0.193 r_symmetry_vdw_refined 0.179 r_nbtor_refined 0.176 r_mcbond_other 0.146 r_symmetry_hbond_refined 0.114 r_metal_ion_refined 0.111 r_xyhbond_nbd_refined 0.11 r_nbtor_other 0.085 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6749 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 66
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling