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Structure of plasmepsin II in complex of an pepstatin analogue
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.79 67.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.154 α = 90 b = 141.154 β = 90 c = 97.375 γ = 120
Symmetry Space Group P 31 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.8 119.52 95.5 0.119 3.9 27929 27929
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.8 57 25357 25357 1353 95.65 0.21884 0.21884 0.21623 0.2087 0.26796 0.2589 RANDOM 58.963
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] 4.03 2.02 4.03 -6.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.658 r_mcangle_it 2.459 r_scangle_it 2.036 r_angle_refined_deg 1.514 r_mcbond_it 1.425 r_scbond_it 1.307 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.658 r_mcangle_it 2.459 r_scangle_it 2.036 r_angle_refined_deg 1.514 r_mcbond_it 1.425 r_scbond_it 1.307 r_symmetry_vdw_refined 0.227 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.103 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5214 Nucleic Acid Atoms Solvent Atoms 37 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing