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Crystal structure of alkaline nuclease from Herpes simplex virus-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277.15 Ammonium sulfate, Sodium acetate, PEG 4000, Glycerol and DMSO
Crystal Properties Matthews coefficient Solvent content 2.6 52.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.997 α = 90 b = 80.233 β = 90 c = 127.572 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 100 PIXEL DECTRIS EIGER X 9M KB bimorph mirrors 2024-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-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 2.46 29.642 99.9 0.037 0.052 0.037 0.999 13.8 1.9 22700
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.46 2.56 99.2 0.316 0.316 0.446 0.885 2.4 1.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.46 29.642 22644 1104 99.876 0.184 0.1809 0.182 0.2378 0.2395 61.938
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] 7.233 -3 -4.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.509 r_dihedral_angle_6_deg 14.39 r_lrange_other 14.004 r_lrange_it 13.989 r_scangle_it 12.458 r_scangle_other 12.399 r_dihedral_angle_2_deg 10.319 r_mcangle_it 10.024 r_mcangle_other 10.021 r_scbond_it 8.945
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.509 r_dihedral_angle_6_deg 14.39 r_lrange_other 14.004 r_lrange_it 13.989 r_scangle_it 12.458 r_scangle_other 12.399 r_dihedral_angle_2_deg 10.319 r_mcangle_it 10.024 r_mcangle_other 10.021 r_scbond_it 8.945 r_scbond_other 8.84 r_dihedral_angle_1_deg 7.319 r_mcbond_other 7.299 r_mcbond_it 7.298 r_angle_refined_deg 2.247 r_angle_other_deg 0.754 r_symmetry_nbd_refined 0.326 r_nbd_refined 0.229 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.192 r_symmetry_xyhbond_nbd_other 0.185 r_nbd_other 0.151 r_xyhbond_nbd_refined 0.15 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.09 r_symmetry_xyhbond_nbd_refined 0.038 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3317 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement FAST_DP data reduction Aimless data scaling PHASER phasing