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Crystal structure of endoglycoceramidase I from Rhodococ-cus equi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 PEG 6000 MES sodium hydroxide Ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.4 48.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 192.841 α = 90 b = 48.98 β = 114.3 c = 120.304 γ = 90
Symmetry Space Group C 1 2 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 315r 2015-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.108 50 98.4 10.09 4.2 58536
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 96 4.3
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 2OSW 2.11 50 55593 2943 97.9 0.186 0.184 0.1936 0.218 0.2242 RANDOM 22.21
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] -0.91 -0.63 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.655 r_dihedral_angle_4_deg 17.545 r_dihedral_angle_3_deg 13.265 r_dihedral_angle_1_deg 5.727 r_long_range_B_refined 3.132 r_long_range_B_other 3.132 r_scangle_other 1.129 r_mcangle_it 1.122 r_mcangle_other 1.122 r_angle_refined_deg 1.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.655 r_dihedral_angle_4_deg 17.545 r_dihedral_angle_3_deg 13.265 r_dihedral_angle_1_deg 5.727 r_long_range_B_refined 3.132 r_long_range_B_other 3.132 r_scangle_other 1.129 r_mcangle_it 1.122 r_mcangle_other 1.122 r_angle_refined_deg 1.073 r_angle_other_deg 0.746 r_scbond_it 0.638 r_scbond_other 0.638 r_mcbond_it 0.619 r_mcbond_other 0.619 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6803 Nucleic Acid Atoms Solvent Atoms 467 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing