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Crystal structure of Plasmodium falciparum GRP78-NBD in complex with 7-Deaza-2'-C-methyladenosine
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 3.57 65.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.265 α = 90 b = 84.265 β = 90 c = 291.778 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 2018-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9792 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.88 50 99.9 0.056 35.2 18.9 51027
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 5.61 0.43
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 1.88 45.62 48462 2564 99.93 0.18885 0.18738 0.1966 0.21638 0.2219 RANDOM 30.408
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] 0.76 0.38 0.76 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.299 r_dihedral_angle_4_deg 24.385 r_dihedral_angle_3_deg 15.167 r_long_range_B_refined 8.133 r_long_range_B_other 8.116 r_scangle_other 7.063 r_dihedral_angle_1_deg 6.097 r_scbond_other 4.717 r_scbond_it 4.715 r_mcangle_it 3.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.299 r_dihedral_angle_4_deg 24.385 r_dihedral_angle_3_deg 15.167 r_long_range_B_refined 8.133 r_long_range_B_other 8.116 r_scangle_other 7.063 r_dihedral_angle_1_deg 6.097 r_scbond_other 4.717 r_scbond_it 4.715 r_mcangle_it 3.628 r_mcangle_other 3.62 r_mcbond_it 2.949 r_mcbond_other 2.948 r_angle_refined_deg 1.781 r_angle_other_deg 1.458 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 278 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing