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Major aspartyl peptidase 1 from C. neoformans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6R61
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 protein (83 mg/mL) in 50 mM sodium acetate, pH 5.0, 100 mM sodium chloride with reservoir solution composed of 200 mM lithium sulfate, 45% (v/v) PEG-400, 100 mM sodium acetate pH 4.5.
Crystal Properties Matthews coefficient Solvent content 3.33 63.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.36 α = 90 b = 112.641 β = 90 c = 91.031 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 300K 2018-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.54187
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 73.66 84.3 0.087 0.101 0.997 11.68 3.529 39317 24.365
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.91 29.8 0.565 0.771 0.59 0.99 1.252
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 FOURIER SYNTHESIS THROUGHOUT 6R61 1.8 73.66 37608 1710 84.27 0.1785 0.1772 0.1907 0.207 0.2181 RANDOM 24.601
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 0.98 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.341 r_dihedral_angle_4_deg 18.038 r_dihedral_angle_3_deg 11.317 r_dihedral_angle_1_deg 7.143 r_angle_refined_deg 1.597 r_angle_other_deg 1.01 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.341 r_dihedral_angle_4_deg 18.038 r_dihedral_angle_3_deg 11.317 r_dihedral_angle_1_deg 7.143 r_angle_refined_deg 1.597 r_angle_other_deg 1.01 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2594 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 179
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction