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X-ray crystal structure of 311R Fab in complex with the PfCSP peptide NPNA-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6AXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.04 M KH2PO4, 20% Glycerol, and 16% PEG3000
Crystal Properties Matthews coefficient Solvent content 2.85 56.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.412 α = 90 b = 70.765 β = 90 c = 170.246 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 EIGER X 16M 2022-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.979 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 44.27 99.8 0.055 0.99 17.2 3.3 44216
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 1.9 1.94 97.6 0.96 2.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6AXK 1.9 44.27 44095 2192 99.726 0.186 0.1839 0.1938 0.2216 0.2273 37.602
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] 1.15 -0.472 -0.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 22.382 r_dihedral_angle_3_deg 14.817 r_lrange_it 7.86 r_lrange_other 7.828 r_dihedral_angle_1_deg 7.586 r_scangle_it 6.213 r_scangle_other 6.212 r_mcangle_other 4.821 r_mcangle_it 4.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.624 r_dihedral_angle_4_deg 22.382 r_dihedral_angle_3_deg 14.817 r_lrange_it 7.86 r_lrange_other 7.828 r_dihedral_angle_1_deg 7.586 r_scangle_it 6.213 r_scangle_other 6.212 r_mcangle_other 4.821 r_mcangle_it 4.818 r_scbond_it 4.276 r_scbond_other 4.275 r_mcbond_it 3.584 r_mcbond_other 3.569 r_angle_refined_deg 1.718 r_angle_other_deg 1.408 r_nbd_refined 0.193 r_symmetry_nbd_other 0.188 r_symmetry_nbd_refined 0.188 r_nbd_other 0.173 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.153 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms Solvent Atoms 174 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building PHASER phasing Aimless data reduction pointless data reduction