☰ Navigation Tabs
Crystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279 complexed with sulfate.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4M3N PDB ENTRY 4M3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 0.1M citrte, pH 4.0, 0.8M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.403 α = 90 b = 189.103 β = 90 c = 152.235 γ = 90
Symmetry Space Group C 2 2 21
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 RAYONIX MX225HE 2013-08-12 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9791 APS 31-ID
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 2.16 50 99.1 0.143 8.1 6.7 44423
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 2.16 2.2 93.2 0.429 5.1 2089
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 PDB ENTRY 4M3N 2.16 32.56 44335 2239 99.04 0.1903 0.1884 0.1878 0.2256 0.2253 RANDOM 33.8488
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] 44.46 -15.22 -29.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.457 r_dihedral_angle_4_deg 15.201 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_1_deg 5.862 r_mcangle_it 2.496 r_scbond_it 2.123 r_mcbond_it 1.435 r_angle_refined_deg 1.194 r_chiral_restr 0.081 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.457 r_dihedral_angle_4_deg 15.201 r_dihedral_angle_3_deg 14.611 r_dihedral_angle_1_deg 5.862 r_mcangle_it 2.496 r_scbond_it 2.123 r_mcbond_it 1.435 r_angle_refined_deg 1.194 r_chiral_restr 0.081 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5361 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 56
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction