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Crystal structure of E.coli purine nucleoside phosphorylase with acycloguanosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RJ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 294 ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 3.21 61.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.03 α = 90 b = 120.03 β = 90 c = 238.141 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS PILATUS3 6M 2015-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.32 30 98.66 0.097 7.004 5.55 44040
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.45 93.72 0.28 2.66 3.68
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 4RJ2 2.32 29.95 41823 2152 98.5 0.17806 0.17613 0.1846 0.21664 0.2237 RANDOM 32.911
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 30.928 r_dihedral_angle_4_deg 21.145 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 7.005 r_long_range_B_refined 5.65 r_long_range_B_other 5.639 r_scangle_other 3.724 r_mcangle_it 3.419 r_mcangle_other 3.418 r_scbond_it 2.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.928 r_dihedral_angle_4_deg 21.145 r_dihedral_angle_3_deg 15.514 r_dihedral_angle_1_deg 7.005 r_long_range_B_refined 5.65 r_long_range_B_other 5.639 r_scangle_other 3.724 r_mcangle_it 3.419 r_mcangle_other 3.418 r_scbond_it 2.212 r_scbond_other 2.208 r_mcbond_it 2.022 r_mcbond_other 2.021 r_angle_refined_deg 1.495 r_angle_other_deg 0.97 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5391 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing