☰ Navigation Tabs
Crystal Structure of AgcA bound to 4-ethylguaiacol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20 % PEG 6000, 0.2 M CaCl2 and 0.1 M MES at pH = 6.0
Crystal Properties Matthews coefficient Solvent content 2.58 52.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.559 α = 90 b = 72.559 β = 90 c = 348.502 γ = 90
Symmetry Space Group P 41 21 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 2021-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8153 Diamond I03
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 1.82 50.76 99.91 0.2547 0.2603 0.05285 0.996 7.63 23.2 85027
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 1.82 1.885 99.81 2.375 2.431 0.5122 0.658 0.83 22.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.82 50.76 85014 4313 99.91 0.161 0.1591 0.1599 0.2045 0.2059 24.203
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] 0.78 0.78 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.966 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_2_deg 7.264 r_lrange_it 6.677 r_dihedral_angle_1_deg 6.196 r_lrange_other 6.151 r_scangle_it 5.034 r_scangle_other 5.034 r_scbond_it 3.545 r_scbond_other 3.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.966 r_dihedral_angle_3_deg 12.758 r_dihedral_angle_2_deg 7.264 r_lrange_it 6.677 r_dihedral_angle_1_deg 6.196 r_lrange_other 6.151 r_scangle_it 5.034 r_scangle_other 5.034 r_scbond_it 3.545 r_scbond_other 3.545 r_mcangle_other 3.266 r_mcangle_it 3.263 r_mcbond_it 2.415 r_mcbond_other 2.411 r_angle_refined_deg 2.068 r_angle_other_deg 0.721 r_symmetry_nbd_refined 0.269 r_xyhbond_nbd_refined 0.258 r_nbd_refined 0.237 r_symmetry_xyhbond_nbd_refined 0.211 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.184 r_nbd_other 0.151 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6218 Nucleic Acid Atoms Solvent Atoms 1033 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing