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Crystal structure of calf spleen purine nucleoside phosphorylase complexed to a novel purine analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A9R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 291 31-35% PEG-400 IN 100 MM HEPES OR TRIS BUFFER, PH 7.8-8.2; 100 MM MGCL2; 1% OCTYL-BETA-D-GLUCOPYRANOSIDE , pH 8.0, VAPOR DIFFUSION, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.16 43.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.442 α = 90 b = 93.442 β = 90 c = 93.442 γ = 90
Symmetry Space Group P 21 3
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 4 mirrors 2002-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 0.98 SRS PX14.2
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 2.1 66.074 97.3 0.078 0.078 7.5 4.9 15761
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) 2.1 2.21 84.2 0.21 0.21 3.2 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1a9r 2.1 46.73 14936 786 97.38 0.17015 0.16777 0.1689 0.21759 0.2184 RANDOM 18.21
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 37.785 r_dihedral_angle_4_deg 19.903 r_dihedral_angle_3_deg 15.407 r_dihedral_angle_1_deg 6.577 r_scangle_it 4.083 r_scbond_it 2.509 r_mcangle_it 1.576 r_angle_refined_deg 1.492 r_mcbond_it 0.982 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.785 r_dihedral_angle_4_deg 19.903 r_dihedral_angle_3_deg 15.407 r_dihedral_angle_1_deg 6.577 r_scangle_it 4.083 r_scbond_it 2.509 r_mcangle_it 1.576 r_angle_refined_deg 1.492 r_mcbond_it 0.982 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.305 r_nbd_refined 0.213 r_symmetry_vdw_refined 0.209 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.097 r_bond_refined_d 0.016 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 2082 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 18
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing