☰ Navigation Tabs
Crystal structure of human purine nucleoside phosphorylase in complex with 7-deazaguanine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V41
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 Hanging drops were prepared mixing 1 microL of protein solution and 1 microL of reservoir solution containing 19% ammonium sulfate and 0.5 M sodium citrate pH 5.6. , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.59 73.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.748 α = 90 b = 138.748 β = 90 c = 159.366 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 MAR CCD 165 mm 2008-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.4310 LNLS D03B-MX1
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 2.75 47.95 99.1 0.081 0.081 11 3.9 14793 2 2 65
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) 2.75 99.1 0.081 0.081 3.91 3.9 15340
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1V41 2.75 43.69 2 2 14566 765 98.66 0.2123 0.2123 0.20933 0.2072 0.2693 0.2638 RANDOM 43.404
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.43 r_dihedral_angle_4_deg 26.683 r_dihedral_angle_3_deg 25.884 r_dihedral_angle_1_deg 12.423 r_scangle_it 5.604 r_scbond_it 3.767 r_angle_refined_deg 3.57 r_mcangle_it 2.837 r_mcbond_it 1.751 r_nbtor_refined 0.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.43 r_dihedral_angle_4_deg 26.683 r_dihedral_angle_3_deg 25.884 r_dihedral_angle_1_deg 12.423 r_scangle_it 5.604 r_scbond_it 3.767 r_angle_refined_deg 3.57 r_mcangle_it 2.837 r_mcbond_it 1.751 r_nbtor_refined 0.368 r_nbd_refined 0.322 r_symmetry_vdw_refined 0.262 r_chiral_restr 0.226 r_xyhbond_nbd_refined 0.226 r_symmetry_hbond_refined 0.21 r_bond_refined_d 0.04 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2251 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 26
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement MOSFLM data reduction SCALA data scaling