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S1 nuclease from Aspergillus oryzae in complex with phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.07 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.765 α = 90 b = 62.307 β = 106.75 c = 48.003 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 100 PIXEL DECTRIS PILATUS 6M 2013-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91842 BESSY 14.1
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 1.8 45.97 95.3 0.074 11.7 3.1 20922 17.6
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 1.8 1.84 69 0.386 2.2 2.2
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 1AK0 1.8 45.97 20820 1078 94.86 0.15304 0.15202 0.1623 0.19864 0.1836 Random selection 21.293
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] -1.45 -1.36 -0.52 2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.358 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_3_deg 13.868 r_dihedral_angle_1_deg 6.159 r_long_range_B_refined 4.4 r_long_range_B_other 4.213 r_scangle_other 2.812 r_mcangle_it 1.969 r_mcangle_other 1.969 r_scbond_it 1.909
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.358 r_dihedral_angle_4_deg 14.398 r_dihedral_angle_3_deg 13.868 r_dihedral_angle_1_deg 6.159 r_long_range_B_refined 4.4 r_long_range_B_other 4.213 r_scangle_other 2.812 r_mcangle_it 1.969 r_mcangle_other 1.969 r_scbond_it 1.909 r_scbond_other 1.908 r_angle_refined_deg 1.688 r_mcbond_it 1.433 r_mcbond_other 1.431 r_angle_other_deg 1.066 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2042 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building