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Nuclease NucB from Bacillus licheniformis in P21 space group
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, HANGING DROP 4.6 291 1.8 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, soaked in 0.02 M 3'-AMP
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 23.228 α = 90 b = 47.821 β = 90.75 c = 100.234 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 2013-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.98148 BESSY 14.1
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 1.7 47.82 91.1 0.031 0.037 0.026 0.999 21.8 3.1 22140 -3 14.6
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 1.7 1.73 75.2 0.09 0.114 0.078 0.99 8.3 2.7
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 FREE R-VALUE 6EJS 1.7 47.82 22121 1089 90.69 0.197 0.196 0.2055 0.244 0.2062 RANDOM 20.2163
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] 0.36 0.58 -0.74 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.481 r_dihedral_angle_4_deg 15.146 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 5.828 r_angle_other_deg 3.748 r_mcangle_it 2.428 r_angle_refined_deg 1.759 r_mcbond_it 1.604 r_mcbond_other 1.597 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.481 r_dihedral_angle_4_deg 15.146 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 5.828 r_angle_other_deg 3.748 r_mcangle_it 2.428 r_angle_refined_deg 1.759 r_mcbond_it 1.604 r_mcbond_other 1.597 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_other 0.014 r_gen_planes_refined 0.009 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1676 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing