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Crystal structure of a putative purine nucleoside phosphorylase from Vibrio fischeri ES114 (Target NYSGRC-029521)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 10.5 298 Protein (20mM HEPES pH7.5, 150mM NaCl, 5% glycerol, and 5mM DTT), Reservoir (MCSG2 #05 - 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH pH 10.5, 1.2 M NaH2PO4/0.8 M K2HPO4), Cryoprotection (33% Ethylene glycol), VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.95 36.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.115 α = 90 b = 163.115 β = 90 c = 45.339 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 RAYONIX MX225HE MIRRORS 2013-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979310 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 1.48 40 99.7 0.112 23.7 14.8 37977 12
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 1.48 1.51 96.8 0.801 3.7 13.5 1837
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.48 30.84 37970 1896 99.67 0.1636 0.1624 0.1614 0.187 0.1866 RANDOM 18.3874
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] -0.62 -0.62 -0.62 2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.118 r_dihedral_angle_4_deg 18.066 r_dihedral_angle_3_deg 12.397 r_dihedral_angle_1_deg 6.004 r_mcangle_it 2.119 r_angle_refined_deg 1.636 r_mcbond_it 1.251 r_mcbond_other 1.248 r_angle_other_deg 0.768 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.118 r_dihedral_angle_4_deg 18.066 r_dihedral_angle_3_deg 12.397 r_dihedral_angle_1_deg 6.004 r_mcangle_it 2.119 r_angle_refined_deg 1.636 r_mcbond_it 1.251 r_mcbond_other 1.248 r_angle_other_deg 0.768 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection XDS data reduction Aimless data scaling SHELX phasing SHELXD phasing SHELXE model building