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Recombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate analogue inhibitor 9-(5',5'-difluoro-5'-phosphonopentyl)-9-deazaguanine structure in a new space group with one full trimer in the asymmetric unit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LVU PDB ENTRY 1LVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.7 298 33% PEG 400, 0.1M SODIUM AZIDE, 0.1M HEPES, 0.1M MAGNESIUM CHLORIDE, 1% OCTYL BETA-D-GLUCOPYRANOSIDE, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.6 52.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.795 α = 90 b = 78.253 β = 97.19 c = 94.901 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 100 CCD MARRESEARCH BENT MIRROR 2007-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 1.0500 MPG/DESY, HAMBURG BW6
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 1.45 10 99.4 0.082 4.4 3.3 173360 173360 16
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 1.45 1.53 99.9 0.236 3 2.6 25329
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LVU 1.45 10 173360 173360 8787 99.31 0.18095 0.18095 0.17999 0.1879 0.19933 THIN RESIOLUTION SHELLS 16.41
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] -0.05 0.13 -0.26 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.674 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_1_deg 5.847 r_angle_other_deg 3.683 r_scangle_it 3.264 r_scbond_it 2.071 r_angle_refined_deg 1.386 r_mcangle_it 1.369 r_mcbond_it 0.782
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.674 r_dihedral_angle_4_deg 17.384 r_dihedral_angle_3_deg 13.148 r_dihedral_angle_1_deg 5.847 r_angle_other_deg 3.683 r_scangle_it 3.264 r_scbond_it 2.071 r_angle_refined_deg 1.386 r_mcangle_it 1.369 r_mcbond_it 0.782 r_symmetry_vdw_refined 0.331 r_symmetry_vdw_other 0.27 r_nbd_other 0.246 r_nbd_refined 0.21 r_nbtor_refined 0.179 r_nbtor_other 0.106 r_xyhbond_nbd_refined 0.103 r_chiral_restr 0.093 r_symmetry_hbond_refined 0.062 r_bond_refined_d 0.012 r_gen_planes_other 0.007 r_symmetry_metal_ion_refined 0.007 r_gen_planes_refined 0.006 r_metal_ion_refined 0.004 r_bond_other_d r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other 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 6456 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 72
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling