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Endo-glycoceramidase II from Rhodococcus sp.: five-membered iminocyclitol 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 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.786 α = 90 b = 93.282 β = 98.3 c = 94.471 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 2006-03-24 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 1.841 18.3 91.9 0.048 0.048 14.1 4 72622 21.22
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) 1.841 1.95 75.4 0.346 0.346 2.2 3.9 8650
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OSW 1.86 18.3 72620 3701 93.43 0.182 0.18 0.212 0.2002 RANDOM 16.128
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] 1.09 -0.16 0.46 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.677 r_dihedral_angle_3_deg 12.039 r_dihedral_angle_4_deg 9.876 r_dihedral_angle_1_deg 5.98 r_scangle_it 1.92 r_scbond_it 1.219 r_angle_refined_deg 1.196 r_angle_other_deg 0.894 r_mcangle_it 0.88 r_mcbond_it 0.492
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.677 r_dihedral_angle_3_deg 12.039 r_dihedral_angle_4_deg 9.876 r_dihedral_angle_1_deg 5.98 r_scangle_it 1.92 r_scbond_it 1.219 r_angle_refined_deg 1.196 r_angle_other_deg 0.894 r_mcangle_it 0.88 r_mcbond_it 0.492 r_nbd_other 0.192 r_nbd_refined 0.191 r_nbtor_refined 0.176 r_symmetry_vdw_other 0.149 r_mcbond_other 0.147 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.125 r_symmetry_vdw_refined 0.109 r_metal_ion_refined 0.092 r_nbtor_other 0.083 r_chiral_restr 0.064 r_bond_refined_d 0.009 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 6773 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 46
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction CCP4 data scaling