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Crystal structure of Plasmodium falciparum GRP78-NBD in complex with VER155008
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 298 0.7 M (NH4)2SO4, 1.2 M Li2SO4, 0.1 M NaCitrate, pH 5.6
Crystal Properties Matthews coefficient Solvent content 3.36 63.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.997 α = 90 b = 83.997 β = 90 c = 292.603 γ = 120
Symmetry Space Group P 65 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 2021-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0332 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) 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 1.75 50 100 0.06 0.06 32.2 19 62702
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.86 0.51 0.53
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 5UMB 1.75 48.81 59614 3085 99.97 0.20146 0.20065 0.2101 0.21699 0.2119 RANDOM 25.202
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] 0.75 0.38 0.75 -2.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.464 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 13.539 r_long_range_B_refined 6.699 r_long_range_B_other 6.64 r_dihedral_angle_1_deg 6.184 r_scangle_other 5.694 r_scbond_it 3.87 r_scbond_other 3.864 r_mcangle_it 2.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.464 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 13.539 r_long_range_B_refined 6.699 r_long_range_B_other 6.64 r_dihedral_angle_1_deg 6.184 r_scangle_other 5.694 r_scbond_it 3.87 r_scbond_other 3.864 r_mcangle_it 2.919 r_mcangle_other 2.918 r_mcbond_it 2.289 r_mcbond_other 2.281 r_angle_refined_deg 1.86 r_angle_other_deg 1.491 r_chiral_restr 0.092 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2951 Nucleic Acid Atoms Solvent Atoms 302 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing