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Crystal structure of pepstatin A bound histo-aspartic protease (HAP) from Plasmodium falciparum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 15% PEG 20000, 0.1M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 59.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.7 α = 90 b = 70.7 β = 90 c = 158.7 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 IMAGE PLATE MAR scanner 345 mm plate 2008-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.3 40 99.7 0.2 6.6 7374 7350
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.4 99.5 0.885 2.2 6.7 631
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 1SME 3.3 20 6939 366 100 0.288 0.285 0.2851 0.353 0.3543 RANDOM 66.573
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] -0.55 -0.27 -0.55 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.115 r_dihedral_angle_3_deg 22.356 r_dihedral_angle_4_deg 14.072 r_dihedral_angle_1_deg 9.214 r_scangle_it 3.613 r_angle_refined_deg 2.253 r_scbond_it 2.007 r_mcangle_it 1.71 r_mcbond_it 0.902 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.115 r_dihedral_angle_3_deg 22.356 r_dihedral_angle_4_deg 14.072 r_dihedral_angle_1_deg 9.214 r_scangle_it 3.613 r_angle_refined_deg 2.253 r_scbond_it 2.007 r_mcangle_it 1.71 r_mcbond_it 0.902 r_chiral_restr 0.128 r_bond_refined_d 0.024 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2618 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 8
Software Software Software Name Purpose MAR345 data collection MrBUMP phasing REFMAC refinement XDS data reduction XDS data scaling