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Structural analysis of P knowlesi homolog of P falciparum PNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SQ6 pdb entries 1SQ6, 1NW4 experimental model PDB 1NW4 pdb entries 1SQ6, 1NW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 sodium thiosulfate, MOPS, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.5 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.377 α = 90 b = 98.377 β = 90 c = 160.08 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 ADSC QUANTUM 210 2004-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 0.9184 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 41.1693 96.9 0.87 13 7.4 24916 24916 -3 24.193
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.95 81.4 0.781 1.9 4.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entries 1SQ6, 1NW4 1.85 14.99 23591 23591 1257 96.85 0.18859 0.18859 0.18674 0.22498 0.1851 RANDOM 27.461
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 13.175 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_1_deg 5.359 r_scangle_it 4.137 r_scbond_it 3.21 r_mcangle_it 2.826 r_mcbond_it 2.045 r_angle_refined_deg 1.152 r_angle_other_deg 0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.632 r_dihedral_angle_4_deg 13.175 r_dihedral_angle_3_deg 11.334 r_dihedral_angle_1_deg 5.359 r_scangle_it 4.137 r_scbond_it 3.21 r_mcangle_it 2.826 r_mcbond_it 2.045 r_angle_refined_deg 1.152 r_angle_other_deg 0.751 r_mcbond_other 0.473 r_symmetry_vdw_other 0.263 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.194 r_nbd_other 0.171 r_nbtor_refined 0.167 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.14 r_nbtor_other 0.08 r_chiral_restr 0.063 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1807 Nucleic Acid Atoms Solvent Atoms 133 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing