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Endo-glycoceramidase II from Rhodococcus sp.: Lactosyl-Enzyme Intermediate
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 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.947 α = 90 b = 93.687 β = 98.12 c = 94.46 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 2006-03-15 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) 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 2.1 50 99.7 0.061 12.5 4.1 54279 33.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.18 99.5 0.383 4.1 5402
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 2.1 18.73 54001 2757 99.37 0.208 0.205 0.2104 0.251 0.2579 RANDOM 21.719
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] 0.61 -0.13 0.15 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.971 r_dihedral_angle_3_deg 12.974 r_dihedral_angle_4_deg 11.161 r_dihedral_angle_1_deg 6.692 r_scangle_it 2.559 r_scbond_it 1.751 r_angle_refined_deg 1.439 r_mcangle_it 1.159 r_angle_other_deg 0.979 r_mcbond_it 0.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.971 r_dihedral_angle_3_deg 12.974 r_dihedral_angle_4_deg 11.161 r_dihedral_angle_1_deg 6.692 r_scangle_it 2.559 r_scbond_it 1.751 r_angle_refined_deg 1.439 r_mcangle_it 1.159 r_angle_other_deg 0.979 r_mcbond_it 0.654 r_nbd_refined 0.208 r_nbd_other 0.199 r_nbtor_refined 0.177 r_mcbond_other 0.171 r_symmetry_vdw_other 0.17 r_xyhbond_nbd_refined 0.146 r_symmetry_vdw_refined 0.138 r_metal_ion_refined 0.104 r_nbtor_other 0.087 r_chiral_restr 0.08 r_bond_refined_d 0.014 r_symmetry_hbond_refined 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6694 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 46
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling