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Structure of hypothiocyanous acid reductase (Har) from Streptococcus pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q2G0I4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 2.4 M sodium malonate dibasic, pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.32 62.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.259 α = 90 b = 122.259 β = 90 c = 92.439 γ = 90
Symmetry Space Group P 43 21 2
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 EIGER X 16M 2023-08-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 47.1 99.6 0.999 15.2 26.6 110989
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.754
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.5 47.1 105305 5590 99.56 0.15921 0.15797 0.18311 0.1875 RANDOM 23.041
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] 0.08 0.08 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.164 r_dihedral_angle_4_deg 17.129 r_dihedral_angle_3_deg 12.723 r_dihedral_angle_1_deg 6.509 r_long_range_B_refined 6.029 r_scbond_it 3.204 r_mcangle_it 2.687 r_angle_refined_deg 2.028 r_mcbond_it 1.828 r_chiral_restr 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.164 r_dihedral_angle_4_deg 17.129 r_dihedral_angle_3_deg 12.723 r_dihedral_angle_1_deg 6.509 r_long_range_B_refined 6.029 r_scbond_it 3.204 r_mcangle_it 2.687 r_angle_refined_deg 2.028 r_mcbond_it 1.828 r_chiral_restr 0.13 r_bond_refined_d 0.014 r_gen_planes_refined 0.014 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 3343 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement MrBUMP phasing Coot model building XDS data reduction Aimless data scaling