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Structure of saposin B in complex with atovaquone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V2O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M MES, 30% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.96 58.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.707 α = 90 b = 75.707 β = 90 c = 95.475 γ = 120
Symmetry Space Group P 32 2 1
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 2M 2018-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.873 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.91 38.62 91.8 0.057 0.063 0.025 0.999 15.8 5.7 14331
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.927 2.18 71.1 0.416 0.523 0.312 0.825 2.4
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 4V2O 2.38 38.62 12391 715 99.46 0.2349 0.2326 0.2405 0.2777 0.2809 RANDOM 76.973
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] 0.08 0.04 0.08 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.322 r_dihedral_angle_3_deg 15.339 r_dihedral_angle_4_deg 8.571 r_dihedral_angle_1_deg 4.964 r_angle_refined_deg 1.343 r_angle_other_deg 1.27 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.322 r_dihedral_angle_3_deg 15.339 r_dihedral_angle_4_deg 8.571 r_dihedral_angle_1_deg 4.964 r_angle_refined_deg 1.343 r_angle_other_deg 1.27 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1835 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing