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The structure of Plasmodium vivax Duffy binding protein (PvDBP) bound to human antibody DB9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NUV 4NUV and 3DIF experimental model PDB 3DIF 4NUV and 3DIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 45 % v/v polypropylene glycol 400, 10% v/v ethanol
Crystal Properties Matthews coefficient Solvent content 4.07 69.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.56 α = 90 b = 173.56 β = 90 c = 169.73 γ = 120
Symmetry Space Group P 62 2 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 2017-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97625 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 42.04 100 12.8 19.6 30707 109.78
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.09
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 4NUV and 3DIF 3.04 42.04 30707 1550 99.9 0.204 0.202 0.1982 0.238 0.2361 RANDOM 115.38
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] 16.9122 16.9122 -33.8244
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.5 t_omega_torsion 2.89 t_angle_deg 1.36 t_bond_d 0.015 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 20.5 t_omega_torsion 2.89 t_angle_deg 1.36 t_bond_d 0.015 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 5752 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing