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Crystal structure of proplasmepsin from the human malarial pathogen Plasmodium vivax
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QS8 PDB entries 1QS8 and 1PFZ experimental model PDB 1PFZ PDB entries 1QS8 and 1PFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 294 18% PEG 4000, 100 mM Tris, 200 mM ammonium acetate, 3% t-amyl alcohol, 15 % glycerol, pH 8.0, VAPOR DIFFUSION, SITTING
DROP, temperature 394K
Crystal Properties Matthews coefficient Solvent content 3.07 59.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.409 α = 90 b = 92.735 β = 130.11 c = 99.132 γ = 90
Symmetry Space Group C 1 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 90 IMAGE PLATE MARRESEARCH 1997-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X12B 0.978 NSLS X12B
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 2.5 30 99.3 0.048 15.5 3.27 117641 116818 1 1 62.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.54 98.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 1QS8 and 1PFZ 2.5 30 1 35657 33805 1852 99.29 0.20535 0.20322 0.24534 0.2823 RANDOM 18.297
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] -1.56 -1.23 3.4 -3.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.684 r_dihedral_angle_1_deg 4.239 r_scangle_it 3.099 r_scbond_it 1.913 r_angle_refined_deg 1.52 r_mcangle_it 1.301 r_mcbond_it 0.687 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.237 r_symmetry_hbond_refined 0.214
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.684 r_dihedral_angle_1_deg 4.239 r_scangle_it 3.099 r_scbond_it 1.913 r_angle_refined_deg 1.52 r_mcangle_it 1.301 r_mcbond_it 0.687 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.237 r_symmetry_hbond_refined 0.214 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5969 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement