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macrocyclase OphP with 15mer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N4C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M sodium acetate, 0.1 M Bis-Tris propane (pH 6.0-6.5) and 28% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.22 α = 113.04 b = 106.18 β = 101.67 c = 114.79 γ = 93.24
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 2021-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 2.47 64.35 98.6 0.12 0.142 0.993 13 3.6 104483
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 2.47 2.51 97.9 1.375 1.618 0.53 0.9 3.6
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 5N4C 2.47 64.35 99258 5223 98.58 0.2311 0.2293 0.2276 0.266 0.264 RANDOM 72.921
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] -1.58 1.03 -0.26 -0.14 1.94 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.672 r_dihedral_angle_4_deg 17.125 r_dihedral_angle_3_deg 15.755 r_dihedral_angle_1_deg 7.616 r_angle_refined_deg 1.464 r_angle_other_deg 1.184 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.672 r_dihedral_angle_4_deg 17.125 r_dihedral_angle_3_deg 15.755 r_dihedral_angle_1_deg 7.616 r_angle_refined_deg 1.464 r_angle_other_deg 1.184 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23176 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 122
Software Software Software Name Purpose XDS data reduction xia2 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction