☰ Navigation Tabs
Structure of subdomain 3 of the Plasmodium vivx Duffy binding protein (PvDBP) bound to human antibody DB9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M ammonium acetate, 0.1M sodium acetate pH 4.0, 15% PEG 4000
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.427 α = 90 b = 126.191 β = 90 c = 129.863 γ = 90
Symmetry Space Group P 21 21 21
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 2017-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9999 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 1.55 90.5 98.3 0.999 14.77 6.5 180370
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 1.55 1.605 0.58
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.55 90.5 178875 8857 98.3 0.2053 0.2044 0.2232 0.2174 RANDOM 30.97
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] 2.7153 -2.0408 -0.6745
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.9 t_omega_torsion 4.34 t_angle_deg 1.12 t_bond_d 0.011 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 14.9 t_omega_torsion 4.34 t_angle_deg 1.12 t_bond_d 0.011 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 8524 Nucleic Acid Atoms Solvent Atoms 978 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing