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Nuclease NucB from Bacillus licheniformis in P1 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EJT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 1.8 M ammonium sulfate, 0.1 M sodium acetate pH 4.6
0.02 M MnCl2 (soaked)
Crystal Properties Matthews coefficient Solvent content 2.4 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.227 α = 75.51 b = 48 β = 89.53 c = 52.203 γ = 89.6
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 2013-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 1.823 BESSY 14.2
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 1.9 46.47 90.1 0.045 0.056 0.034 0.979 19.1 4.7 15502 -3 21.43
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 1.9 1.94 64.6 0.182 0.236 0.148 0.639 5.4 3.9
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 6ejt 1.9 46.47 15489 795 90.04 0.1738 0.1736 0.1829 0.1767 0.1866 RANDOM 25.4376
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] 0.26 0.34 -1.05 -0.12 0.77 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_4_deg 14.27 r_dihedral_angle_3_deg 13.366 r_dihedral_angle_1_deg 5.739 r_angle_other_deg 3.733 r_mcangle_it 2.786 r_mcbond_it 1.892 r_mcbond_other 1.855 r_angle_refined_deg 1.67 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_4_deg 14.27 r_dihedral_angle_3_deg 13.366 r_dihedral_angle_1_deg 5.739 r_angle_other_deg 3.733 r_mcangle_it 2.786 r_mcbond_it 1.892 r_mcbond_other 1.855 r_angle_refined_deg 1.67 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1676 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing