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Structure of Plasmodium falciparum P113 bound to antibody P3.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U0R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2M NH4SO4, 0.1M MES pH=6.5, 20% w/v PEG8000
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.921 α = 90 b = 96.921 β = 90 c = 177.898 γ = 90
Symmetry Space Group P 41 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 PILATUS3 6M 2017-12-04 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) Rpim I (All) 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 1.95 96.92 100 0.042 0.994 16.6 26.2 1636680 62581
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 100 1.422 0.571 1.7 26.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4U0R 1.95 96.92 62481 3110 100 0.2058 0.2047 0.2096 0.2257 0.2349 RANDOM 43.14
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] 4.2067 4.2067 -8.4135
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.15 t_omega_torsion 6.33 t_angle_deg 1.13 t_bond_d 0.013 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.15 t_omega_torsion 6.33 t_angle_deg 1.13 t_bond_d 0.013 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4929 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 5
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction autoPROC data reduction xia2 data scaling PHASER phasing