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Crystal Structure of NlpC/P60 domain from Clostridium innocuum NlpC/P60 domain-containing protein CI_01448.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 292 Protein: 10.0 mg/ml, 0.25M Sodium chloride, 0.01M Tris pH 8.3;
Screen: AmSO4 (G4), 1.0M Ammonium sulfate, 0.1M HEPES sodium salt pH 5.6, 2% (w/v) PEG 400;
Cryo: 2M Lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.954 α = 90 b = 51.954 β = 90 c = 157.44 γ = 120
Symmetry Space Group P 31 2 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 CCD MARMOSAIC 300 mm CCD BE 2020-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.92 30 99.9 0.137 0.137 0.149 0.058 0.988 15.2 6.5 19632 -3 21.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.92 1.95 99.8 0.856 0.856 0.928 0.357 0.779 2.6 6.5
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 1.92 29.62 18593 995 99.89 0.1584 0.1561 0.156 0.203 0.2021 RANDOM 22.028
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] 0.37 0.18 0.37 -1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.972 r_dihedral_angle_4_deg 10.612 r_dihedral_angle_3_deg 8.208 r_dihedral_angle_1_deg 3.946 r_angle_refined_deg 1.311 r_angle_other_deg 0.338 r_chiral_restr 0.059 r_gen_planes_refined 0.055 r_gen_planes_other 0.05 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.972 r_dihedral_angle_4_deg 10.612 r_dihedral_angle_3_deg 8.208 r_dihedral_angle_1_deg 3.946 r_angle_refined_deg 1.311 r_angle_other_deg 0.338 r_chiral_restr 0.059 r_gen_planes_refined 0.055 r_gen_planes_other 0.05 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1734 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing