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Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LA8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M MES:NaOH, pH 6.5, 1.6 Magnesium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.95 α = 103.42 b = 81.06 β = 105.36 c = 91.616 γ = 112.73
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 2013-07-18 SINGLE WAVELENGTH
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 1.9 50 97 0.113 9.7 2.1 148934
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 1.9 1.93 94.3 0.718 2 7253
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 3LA8 1.9 20 146913 7374 97.07 0.2154 0.2132 0.2131 0.2575 0.2564 RANDOM 34.4156
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] -0.07 0.66 0.46 -0.26 0.78 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.245 r_dihedral_angle_4_deg 20.427 r_dihedral_angle_3_deg 15.844 r_dihedral_angle_1_deg 5.751 r_scbond_it 2.72 r_mcangle_it 2.644 r_mcbond_it 1.624 r_angle_refined_deg 1.424 r_chiral_restr 0.093 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.245 r_dihedral_angle_4_deg 20.427 r_dihedral_angle_3_deg 15.844 r_dihedral_angle_1_deg 5.751 r_scbond_it 2.72 r_mcangle_it 2.644 r_mcbond_it 1.624 r_angle_refined_deg 1.424 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12435 Nucleic Acid Atoms Solvent Atoms 662 Heterogen Atoms 144
Software Software Software Name Purpose SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction