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N-terminal domain of EcoKMcrA restriction endonuclease (NEco) in complex with T5hmCGA target sequence
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 1.8 ul of protein-DNA solution (436:523 uM) was mixed with 2.2 ul of the F1 condition of the PACT premier crystal screen (MDL) (0.2 M Sodium fluoride, 0.1 M Bis-Tris propane, pH 6.5, 20% PEG 3350) and cryo-protected with an addition of 25% glycerol.
Crystal Properties Matthews coefficient Solvent content 3.09 60.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.417 α = 90 b = 113.417 β = 90 c = 156.367 γ = 120
Symmetry Space Group P 61 2 2
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 16M 2019-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.9195 PETRA III, EMBL c/o DESY P14 (MX2)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.21 33.54 99.2 0.084 0.086 1 38.15 35.8 30298 55.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.21 2.34 95.4 1.761 1.802 0.734 1.91 20.8
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 THROUGHOUT 6GHC 2.21 33.54 28708 1534 99.21 0.1592 0.157 0.1629 0.2034 0.2113 RANDOM 53.522
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] -0.31 -0.16 -0.31 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.341 r_dihedral_angle_4_deg 13.773 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 6.284 r_angle_other_deg 1.294 r_angle_refined_deg 1.21 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.341 r_dihedral_angle_4_deg 13.773 r_dihedral_angle_3_deg 12.54 r_dihedral_angle_1_deg 6.284 r_angle_other_deg 1.294 r_angle_refined_deg 1.21 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2320 Nucleic Acid Atoms 816 Solvent Atoms 405 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing ARP/wARP model building PDB_EXTRACT data extraction