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Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to R5.251
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.3M Calcium chloride
0.1M Magnesium formate HCl
22.5% (v/v) PurePEGs Cocktail
Crystal Properties Matthews coefficient Solvent content 2.78 55.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.927 α = 60.535 b = 92.016 β = 72.132 c = 92.492 γ = 79.818
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 2023-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 3.13 59.104 98.6 0.955 0.405 3.7 30110
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 3.23 3.29 0.245
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.234 59.104 30108 1403 98.54 0.257 0.2536 0.2334 0.3268 0.2986 71.736
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] 0.118 0.872 3.203 3.125 0.102 -0.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.774 r_lrange_other 14.729 r_lrange_it 14.725 r_dihedral_angle_6_deg 13.271 r_mcangle_other 9.641 r_mcangle_it 9.638 r_dihedral_angle_1_deg 9.171 r_scangle_it 8.636 r_scangle_other 8.635 r_dihedral_angle_2_deg 5.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.774 r_lrange_other 14.729 r_lrange_it 14.725 r_dihedral_angle_6_deg 13.271 r_mcangle_other 9.641 r_mcangle_it 9.638 r_dihedral_angle_1_deg 9.171 r_scangle_it 8.636 r_scangle_other 8.635 r_dihedral_angle_2_deg 5.99 r_mcbond_it 5.816 r_mcbond_other 5.811 r_scbond_it 5.008 r_scbond_other 5.008 r_angle_refined_deg 1.397 r_angle_other_deg 0.501 r_xyhbond_nbd_refined 0.258 r_nbd_refined 0.251 r_nbd_other 0.219 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.189 r_ncsr_local_group_3 0.176 r_ncsr_local_group_1 0.139 r_symmetry_nbd_refined 0.133 r_ncsr_local_group_2 0.128 r_symmetry_xyhbond_nbd_refined 0.115 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11728 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing