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Crystal structure of the HC7-Glu200Ala mutant complexed to a tetraglycopeptide.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PMU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 PEG 8000
MES
Zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.5 50.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.703 α = 90 b = 91.94 β = 90 c = 99.741 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 S 6M 2022-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9793 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.44 20 100 0.085 0.998 10.1 5.5 140966
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.44 1.52 100 0.931 0.646 1.8 5.4
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 1.44 19.9 135297 5577 99.94 0.17107 0.16984 0.1793 0.20114 0.2079 RANDOM 16.001
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] 0.97 -0.38 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.561 r_dihedral_angle_2_deg 8.984 r_dihedral_angle_1_deg 7.632 r_long_range_B_refined 5.78 r_long_range_B_other 5.543 r_scangle_other 4.27 r_scbond_it 2.915 r_scbond_other 2.915 r_mcangle_it 2.544 r_mcangle_other 2.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.561 r_dihedral_angle_2_deg 8.984 r_dihedral_angle_1_deg 7.632 r_long_range_B_refined 5.78 r_long_range_B_other 5.543 r_scangle_other 4.27 r_scbond_it 2.915 r_scbond_other 2.915 r_mcangle_it 2.544 r_mcangle_other 2.544 r_mcbond_it 1.852 r_mcbond_other 1.852 r_angle_refined_deg 1.669 r_angle_other_deg 0.816 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 5484 Nucleic Acid Atoms Solvent Atoms 840 Heterogen Atoms 245
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing