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Crystal structure of Plasmodium falciparum GRP78 in complex with Toyocamycin
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 3.39 63.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.377 α = 90 b = 84.377 β = 90 c = 292.492 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 2018-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 2.25 50 100 0.1 0.15 26.3 18.9 30363
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 2.25 2.39 100 0.11 0.12
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 2.25 48.8 28860 1501 99.97 0.18292 0.18076 0.1881 0.22574 0.2336 RANDOM 31.325
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] 0.7 0.35 0.7 -2.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.204 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 15.437 r_long_range_B_refined 9.135 r_long_range_B_other 9.115 r_scangle_other 7.748 r_dihedral_angle_1_deg 6.179 r_scbond_it 4.978 r_scbond_other 4.962 r_mcangle_it 3.665
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.204 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 15.437 r_long_range_B_refined 9.135 r_long_range_B_other 9.115 r_scangle_other 7.748 r_dihedral_angle_1_deg 6.179 r_scbond_it 4.978 r_scbond_other 4.962 r_mcangle_it 3.665 r_mcangle_other 3.665 r_mcbond_it 2.737 r_mcbond_other 2.737 r_angle_refined_deg 1.729 r_angle_other_deg 1.412 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 237 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing