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Crystal structure of alpha-1-2-mannosidase from Enterococcus faecalis V583
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5SWI PDB entry 5SWI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.15 M sodium acetate, pH 4.5, 0.8 M sodium phosphate monobasic, 1.2 M potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.69 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.35 α = 90 b = 168.99 β = 90 c = 258.52 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M INSERTION DEVICE 2018-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.15 50 99 0.096 0.111 0.997 11.12 4 190871 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 99.2 0.678 0.703 0.782 1.93 4
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 5SWI 2.15 39.18 181227 9643 98.99 0.15698 0.15527 0.1553 0.18893 0.189 RANDOM 32.837
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] -1.92 0.4 1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.775 r_dihedral_angle_4_deg 17.776 r_dihedral_angle_3_deg 14.547 r_long_range_B_refined 6.794 r_dihedral_angle_1_deg 6.621 r_scbond_it 4.163 r_mcangle_it 3.35 r_mcbond_it 2.544 r_angle_refined_deg 1.511 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.775 r_dihedral_angle_4_deg 17.776 r_dihedral_angle_3_deg 14.547 r_long_range_B_refined 6.794 r_dihedral_angle_1_deg 6.621 r_scbond_it 4.163 r_mcangle_it 3.35 r_mcbond_it 2.544 r_angle_refined_deg 1.511 r_chiral_restr 0.109 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23064 Nucleic Acid Atoms Solvent Atoms 1537 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing