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Apo form of restriction endonuclease NhoI.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NhoI complex with 5-methylcytosine oligo
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 0.1M Tris-BICINE, 20 % v/v Ethylene glycol, 10 % w/v PEG 8000; 0.02 M, 1,6-hexanediol, 0.02 M 1-butanol, 0.02 M 1,2-propanediol, 0.02 M 2-propanol, 0.02 M 1,4-butanediol, 0.02 M 1,3-propanediol
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.48 α = 90 b = 58.76 β = 97.23 c = 75.59 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 2022-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 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 2.65 46.25 99.15 0.1127 0.1224 0.04713 0.997 14.57 6.7 9793 54.22
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 2.65 2.75 99.6 0.83 0.9 0.047 0.85 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.65 38.17 1.38 9788 490 99.17 0.2241 0.2216 0.2705 0.2451 Random selection 74.48
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.0263 f_angle_d 0.8012 f_chiral_restr 0.0516 f_plane_restr 0.0074 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2448 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing