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Structure of human purine nucleoside phosphorylase in complex with L-Immucillin-H
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 1.8 M Ammonium dihydrogen phosphate, 100 mM sodium citrate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 5.11 75.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.457 α = 90 b = 143.457 β = 90 c = 166.248 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 315 2006-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.07200 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 2.9 35 99.9 0.102 0.073 7.5 8.8 14755 14741 82
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 2.9 3 99.3 0.845 0.73 1.4 6.5 1442
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 1rr6 2.9 34.54 14736 14728 745 99.94 0.218 0.218 0.216 0.262 0.2398 RANDOM 71.358
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] 0.13 0.06 0.13 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.405 r_dihedral_angle_3_deg 24.583 r_dihedral_angle_4_deg 24.151 r_dihedral_angle_1_deg 12.518 r_scangle_it 4.281 r_angle_refined_deg 2.953 r_scbond_it 2.748 r_mcangle_it 2.027 r_mcbond_it 1.258 r_nbtor_refined 0.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.405 r_dihedral_angle_3_deg 24.583 r_dihedral_angle_4_deg 24.151 r_dihedral_angle_1_deg 12.518 r_scangle_it 4.281 r_angle_refined_deg 2.953 r_scbond_it 2.748 r_mcangle_it 2.027 r_mcbond_it 1.258 r_nbtor_refined 0.354 r_nbd_refined 0.321 r_symmetry_vdw_refined 0.307 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.181 r_symmetry_hbond_refined 0.101 r_bond_refined_d 0.033 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2223 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 24
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