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Nuclease NucB from Bacillus licheniformis in sulphate free conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EJS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.12 M 1,6-Hexanediol
0.12 M 1-Butanol
0.12 M 1,2-Propanediol
0.12 M 2-Propanol
0.12 M 1,4-Butanediol
0.12 M 1,3-Propanediol
0.1 M Tris and Bicine pH 8.5
12.5 % v/v 2-Methyl-
-2,4,-pentanediol
12.5 % PEG 1000
12.5 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.5 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.44 α = 90 b = 58.47 β = 90 c = 72.45 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 PIXEL Bruker PHOTON II HELIOS MX 2017-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE Excillum MetalJet D2+ 70 kV 1.3418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.75 45.5 99.9 0.09 0.101 0.045 0.998 17.9 9.1 24852 -3 14.48
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 0.872 1.018 0.518 0.78 1.8 7.1
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 6EJS 1.75 45.5 24802 1199 99.83 0.1574 0.1569 0.1713 0.1667 0.1816 RANDOM 22.3148
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] -1.04 -0.42 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.125 r_dihedral_angle_3_deg 13.367 r_dihedral_angle_4_deg 13.255 r_dihedral_angle_1_deg 5.696 r_angle_other_deg 3.691 r_mcangle_it 2.527 r_angle_refined_deg 1.818 r_mcbond_it 1.73 r_mcbond_other 1.719 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.125 r_dihedral_angle_3_deg 13.367 r_dihedral_angle_4_deg 13.255 r_dihedral_angle_1_deg 5.696 r_angle_other_deg 3.691 r_mcangle_it 2.527 r_angle_refined_deg 1.818 r_mcbond_it 1.73 r_mcbond_other 1.719 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_other 0.014 r_gen_planes_refined 0.011 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1676 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing