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Crystal structure of DHPS in complex with an inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6WL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 20 % w/v PEG 3350, 0.2 M Ammonium chloride
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.53 α = 90 b = 107.852 β = 93.133 c = 96.86 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 PIXEL DECTRIS EIGER2 XE 16M 2023-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 1.63 72.01 100 0.997 11.8 7 202950
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 1.63 1.66 100 0.378 0.3
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.63 72.004 198681 1928 97.897 0.18 0.1798 0.2105 0.1867 38.484
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] 2.808 0.483 -0.104 -2.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.247 r_dihedral_angle_4_deg 24.458 r_dihedral_angle_3_deg 14.284 r_lrange_it 8.054 r_lrange_other 8.051 r_scangle_it 6.305 r_scangle_other 6.305 r_dihedral_angle_1_deg 6.195 r_mcangle_it 4.753 r_mcangle_other 4.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.247 r_dihedral_angle_4_deg 24.458 r_dihedral_angle_3_deg 14.284 r_lrange_it 8.054 r_lrange_other 8.051 r_scangle_it 6.305 r_scangle_other 6.305 r_dihedral_angle_1_deg 6.195 r_mcangle_it 4.753 r_mcangle_other 4.752 r_scbond_it 4.325 r_scbond_other 4.324 r_mcbond_it 3.448 r_mcbond_other 3.447 r_angle_refined_deg 1.518 r_angle_other_deg 1.42 r_nbd_other 0.245 r_nbd_refined 0.211 r_symmetry_nbd_refined 0.202 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.155 r_ncsr_local_group_1 0.091 r_ncsr_local_group_4 0.084 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_refined 0.077 r_ncsr_local_group_2 0.075 r_ncsr_local_group_5 0.075 r_ncsr_local_group_3 0.068 r_ncsr_local_group_6 0.061 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9511 Nucleic Acid Atoms Solvent Atoms 940 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XSCALE data scaling PHASER phasing