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macrocyclase OphP with ZPP
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 2.03 39.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.68 α = 116.23 b = 102.65 β = 101.09 c = 110.27 γ = 92.18
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 EIGER2 XE 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 67.799 97.6 0.115 0.136 1 14.3 3.5 175661
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 2.03 92.3 1.099 1.308 0.58 1.099
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5N4C 2 67.799 175602 8559 97.544 0.211 0.209 0.2176 0.2452 0.2523 34.309
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] -0.623 -0.622 -0.449 -0.312 -0.92 1.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.55 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 6.896 r_lrange_it 5.741 r_lrange_other 5.741 r_scangle_it 3.122 r_scangle_other 3.122 r_mcangle_it 2.474 r_mcangle_other 2.474
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.55 r_dihedral_angle_4_deg 15.397 r_dihedral_angle_3_deg 13.503 r_dihedral_angle_1_deg 6.896 r_lrange_it 5.741 r_lrange_other 5.741 r_scangle_it 3.122 r_scangle_other 3.122 r_mcangle_it 2.474 r_mcangle_other 2.474 r_scbond_it 2.019 r_scbond_other 2.019 r_mcbond_it 1.563 r_mcbond_other 1.562 r_angle_refined_deg 1.317 r_angle_other_deg 1.184 r_nbd_other 0.232 r_symmetry_nbd_refined 0.224 r_nbd_refined 0.187 r_symmetry_xyhbond_nbd_refined 0.174 r_symmetry_nbd_other 0.17 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.132 r_ncsr_local_group_3 0.087 r_ncsr_local_group_1 0.079 r_ncsr_local_group_2 0.078 r_ncsr_local_group_5 0.076 r_symmetry_nbtor_other 0.074 r_ncsr_local_group_4 0.073 r_ncsr_local_group_6 0.073 r_symmetry_xyhbond_nbd_other 0.06 r_chiral_restr 0.056 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 22761 Nucleic Acid Atoms Solvent Atoms 1328 Heterogen Atoms 257
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing