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Crystal structure of Plasmodium vivax PNP with sulphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B94 PDB ENTRY 2B94
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 18% PEG 4000, 0.2M LiSO4, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal Properties Matthews coefficient Solvent content 1.85 33.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.749 α = 90 b = 94.749 β = 90 c = 121.254 γ = 120
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 MARMOSAIC 225 mm CCD 2007-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 1.0745 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 67.88 80.5 0.095 0.095 17.6 6 14619 14619 2 26.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.92 49 0.234 0.234 4.3 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB ENTRY 2B94 1.85 33.98 14619 13860 759 80.38 0.193 0.19471 0.19269 0.1933 0.23277 0.2298 RANDOM 24.307
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] -2.66 -1.33 -2.66 3.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.808 r_dihedral_angle_1_deg 20.043 r_dihedral_angle_3_deg 15.7 r_dihedral_angle_4_deg 13.905 r_scangle_it 2.797 r_scbond_it 1.896 r_angle_refined_deg 1.611 r_mcangle_it 1.108 r_mcbond_it 0.712 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.808 r_dihedral_angle_1_deg 20.043 r_dihedral_angle_3_deg 15.7 r_dihedral_angle_4_deg 13.905 r_scangle_it 2.797 r_scbond_it 1.896 r_angle_refined_deg 1.611 r_mcangle_it 1.108 r_mcbond_it 0.712 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.195 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.091 r_bond_refined_d 0.012 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_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1921 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 5
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling