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VcaM4I restriction endonuclease in the absence of DNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 Protein (7.2 mg/ml) in 0.27 M NaCl, 13.5 mM Tris-HCl pH 8.5, 0.2 M sodium malonate and 0.9 mM TCEP was mixed in 1:1 ratio with reservoir solution (1.8 M ammonium sulfate, 0.1 M MES pH 5.25). Perfluoropolyether oil was used as a cryoprotectant.
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.97 α = 90 b = 93.532 β = 90 c = 126.261 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 PILATUS 6M-F 2019-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 1.0064 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.5 30 99.2 0.044 0.046 1 26.06 13.1 107966 32.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.59 98.2 1.062 1.104 0.851 2.27 13.4
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 1.5 28.48 105907 1978 99.2 0.1936 0.1933 0.2004 0.2132 0.2203 RANDOM 33.633
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] -2.14 2.66 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 19.725 r_dihedral_angle_3_deg 12.025 r_dihedral_angle_1_deg 5.837 r_angle_refined_deg 1.131 r_angle_other_deg 0.726 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.035 r_dihedral_angle_4_deg 19.725 r_dihedral_angle_3_deg 12.025 r_dihedral_angle_1_deg 5.837 r_angle_refined_deg 1.131 r_angle_other_deg 0.726 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4957 Nucleic Acid Atoms Solvent Atoms 1025 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling SHELXDE phasing ARP/wARP model building PDB_EXTRACT data extraction