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Structure of Purine Nucleoside Phosphorylase from Anopheles gambiae in complex with DADMe-ImmH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RR6 pdb entry 1RR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.1 M Sodium Acetate, 4.0 M Ammonium Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.78 55.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.718 α = 90 b = 106.718 β = 90 c = 240.388 γ = 90
Symmetry Space Group P 41 21 2
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 315 mirrors 2006-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.97910 NSLS X29A
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 2.2 30 93.1 0.122 0.122 5.5 35 71690 66744
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 2.2 2.28 59.6 0.321 0.276 2.1 6.6
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 (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 1RR6 2.2 8 69683 62111 3301 93.87 0.17726 0.17516 0.1819 0.21667 0.2224 RANDOM 24.719
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.256 r_dihedral_angle_4_deg 21.574 r_dihedral_angle_3_deg 15.428 r_dihedral_angle_1_deg 6.365 r_scangle_it 4.051 r_scbond_it 2.75 r_angle_refined_deg 1.722 r_mcangle_it 1.625 r_mcbond_it 1.064 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.256 r_dihedral_angle_4_deg 21.574 r_dihedral_angle_3_deg 15.428 r_dihedral_angle_1_deg 6.365 r_scangle_it 4.051 r_scbond_it 2.75 r_angle_refined_deg 1.722 r_mcangle_it 1.625 r_mcbond_it 1.064 r_nbtor_refined 0.304 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.138 r_symmetry_hbond_refined 0.122 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 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 6546 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 77
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction