☰ Navigation Tabs
Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like isofagomine 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 2.23 44.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.545 α = 90 b = 92.919 β = 98.32 c = 94.489 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 2006-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9795 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 1.5 53 100 0.089 0.089 4.7 7.3 146070 16.068
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 1.5 1.58 100 0.456 0.456 1.6 7.3 21265
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 1.5 53 146040 7327 99.98 0.178 0.177 0.1824 0.198 0.2045 RANDOM 12.219
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] 0.85 -0.04 0.17 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.378 r_dihedral_angle_3_deg 11.73 r_dihedral_angle_4_deg 9.831 r_dihedral_angle_1_deg 5.706 r_scangle_it 1.623 r_angle_refined_deg 1.068 r_scbond_it 1.031 r_angle_other_deg 0.843 r_mcangle_it 0.738 r_mcbond_it 0.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.378 r_dihedral_angle_3_deg 11.73 r_dihedral_angle_4_deg 9.831 r_dihedral_angle_1_deg 5.706 r_scangle_it 1.623 r_angle_refined_deg 1.068 r_scbond_it 1.031 r_angle_other_deg 0.843 r_mcangle_it 0.738 r_mcbond_it 0.402 r_symmetry_vdw_other 0.271 r_nbd_refined 0.195 r_nbd_other 0.19 r_nbtor_refined 0.177 r_symmetry_vdw_refined 0.123 r_mcbond_other 0.122 r_symmetry_hbond_refined 0.113 r_metal_ion_refined 0.101 r_xyhbond_nbd_refined 0.091 r_nbtor_other 0.083 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 6792 Nucleic Acid Atoms Solvent Atoms 961 Heterogen Atoms 52
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction CCP4 data scaling