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Crystal structure of nucleoside phosphatase Sa1684 complex with ATP analogue from staphylococus aureus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 289.15 20% PEG400, 0.1M sodium citrate pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.2 44.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.298 α = 90 b = 36.478 β = 108.52 c = 56.074 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 CCD ADSC QUANTUM 315r 2017-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 1.2809 SSRF BL17U1
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 1.62 50 99.7 0.07 23.05 7.2 24142
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 1.65 0.96
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 1.62 42.45 22883 1248 99.48 0.1783 0.1773 0.1894 0.1963 0.212 RANDOM 21.087
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] 0.45 -0.28 -0.95 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.368 r_dihedral_angle_4_deg 22.012 r_dihedral_angle_3_deg 13.513 r_dihedral_angle_1_deg 7.619 r_angle_refined_deg 1.713 r_angle_other_deg 1.438 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.368 r_dihedral_angle_4_deg 22.012 r_dihedral_angle_3_deg 13.513 r_dihedral_angle_1_deg 7.619 r_angle_refined_deg 1.713 r_angle_other_deg 1.438 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1477 Nucleic Acid Atoms Solvent Atoms 107 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing