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Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to R5.034
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WAT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.02 M Calcium chloride dihydrate
0.02 M Cadmium chloride hydrate
0.02 M Cobalt(II) chloride hexahydrate
20% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 5.04 75.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.259 α = 90 b = 376.787 β = 90.062 c = 226.818 γ = 90
Symmetry Space Group P 1 2 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 PILATUS3 6M 2023-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
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 3.99 65.604 99 0.993 0.319 6.8 115243
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 3.99 4.06 0.22
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.994 65.604 115176 1918 98.869 0.442 0.4413 0.4415 0.4581 0.4587 RANDOM 166.39
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] -0.609 4.384 2.822 -2.222
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 37.565 r_dihedral_angle_3_deg 17.905 r_mcangle_it 15.724 r_scangle_it 13.044 r_dihedral_angle_6_deg 12.355 r_mcbond_it 8.754 r_dihedral_angle_2_deg 8.6 r_dihedral_angle_1_deg 8.474 r_scbond_it 6.868 r_angle_refined_deg 1.711
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 37.565 r_dihedral_angle_3_deg 17.905 r_mcangle_it 15.724 r_scangle_it 13.044 r_dihedral_angle_6_deg 12.355 r_mcbond_it 8.754 r_dihedral_angle_2_deg 8.6 r_dihedral_angle_1_deg 8.474 r_scbond_it 6.868 r_angle_refined_deg 1.711 r_symmetry_nbd_refined 0.425 r_symmetry_xyhbond_nbd_refined 0.374 r_nbtor_refined 0.294 r_nbd_refined 0.218 r_ncsr_local_group_83 0.187 r_ncsr_local_group_74 0.178 r_ncsr_local_group_5 0.166 r_ncsr_local_group_7 0.165 r_ncsr_local_group_79 0.162 r_ncsr_local_group_77 0.161 r_xyhbond_nbd_refined 0.16 r_ncsr_local_group_2 0.159 r_ncsr_local_group_72 0.159 r_ncsr_local_group_73 0.157 r_ncsr_local_group_6 0.156 r_ncsr_local_group_13 0.156 r_ncsr_local_group_42 0.156 r_ncsr_local_group_1 0.155 r_ncsr_local_group_52 0.154 r_ncsr_local_group_14 0.153 r_ncsr_local_group_53 0.153 r_ncsr_local_group_59 0.152 r_ncsr_local_group_61 0.152 r_ncsr_local_group_3 0.151 r_ncsr_local_group_81 0.151 r_ncsr_local_group_63 0.15 r_ncsr_local_group_62 0.148 r_ncsr_local_group_66 0.148 r_ncsr_local_group_78 0.148 r_ncsr_local_group_11 0.147 r_ncsr_local_group_44 0.146 r_ncsr_local_group_33 0.145 r_ncsr_local_group_40 0.145 r_ncsr_local_group_32 0.144 r_ncsr_local_group_64 0.144 r_ncsr_local_group_22 0.143 r_ncsr_local_group_50 0.143 r_ncsr_local_group_4 0.142 r_ncsr_local_group_58 0.142 r_ncsr_local_group_65 0.142 r_ncsr_local_group_69 0.142 r_ncsr_local_group_84 0.142 r_ncsr_local_group_71 0.14 r_ncsr_local_group_21 0.139 r_ncsr_local_group_35 0.139 r_ncsr_local_group_67 0.139 r_ncsr_local_group_70 0.139 r_ncsr_local_group_39 0.136 r_ncsr_local_group_46 0.136 r_ncsr_local_group_27 0.135 r_ncsr_local_group_54 0.135 r_chiral_restr 0.134 r_ncsr_local_group_30 0.134 r_ncsr_local_group_23 0.133 r_ncsr_local_group_41 0.133 r_ncsr_local_group_24 0.132 r_ncsr_local_group_43 0.132 r_ncsr_local_group_48 0.132 r_ncsr_local_group_76 0.132 r_ncsr_local_group_82 0.131 r_ncsr_local_group_25 0.13 r_ncsr_local_group_36 0.128 r_ncsr_local_group_51 0.128 r_ncsr_local_group_75 0.127 r_ncsr_local_group_45 0.126 r_ncsr_local_group_17 0.124 r_ncsr_local_group_47 0.123 r_ncsr_local_group_37 0.122 r_ncsr_local_group_68 0.122 r_ncsr_local_group_10 0.121 r_ncsr_local_group_38 0.12 r_ncsr_local_group_55 0.12 r_ncsr_local_group_26 0.119 r_ncsr_local_group_12 0.117 r_ncsr_local_group_18 0.117 r_ncsr_local_group_9 0.116 r_ncsr_local_group_49 0.115 r_ncsr_local_group_29 0.114 r_ncsr_local_group_60 0.114 r_ncsr_local_group_20 0.111 r_ncsr_local_group_56 0.111 r_ncsr_local_group_80 0.11 r_ncsr_local_group_31 0.109 r_ncsr_local_group_19 0.108 r_ncsr_local_group_8 0.106 r_ncsr_local_group_15 0.098 r_ncsr_local_group_57 0.098 r_ncsr_local_group_34 0.096 r_ncsr_local_group_28 0.093 r_ncsr_local_group_16 0.086 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32276 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing