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Crystal structure of isomerase PaaG with trans-3,4-didehydroadipyl-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HRX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 50 mM KH2PO4, pH 4.5, 20-22% PEG 3350, 3% (w/v) NDSB-201 and 20% glycerol (v/v)
Crystal Properties Matthews coefficient Solvent content 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.024 α = 90 b = 88.024 β = 90 c = 88.024 γ = 90
Symmetry Space Group P 21 3
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 2019-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.88 44.01 99.41 0.997 22.48 2 18671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.947 0.2998
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 THROUGHOUT 3HRX 1.88 44.01 18665 1013 99.419 0.171 0.1681 0.1776 0.2171 0.2244 35.196
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.763 r_dihedral_angle_4_deg 15.151 r_dihedral_angle_3_deg 14.714 r_lrange_other 7.308 r_lrange_it 7.301 r_dihedral_angle_1_deg 6.878 r_scangle_it 6.054 r_scangle_other 6.052 r_scbond_it 4.075 r_scbond_other 4.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.763 r_dihedral_angle_4_deg 15.151 r_dihedral_angle_3_deg 14.714 r_lrange_other 7.308 r_lrange_it 7.301 r_dihedral_angle_1_deg 6.878 r_scangle_it 6.054 r_scangle_other 6.052 r_scbond_it 4.075 r_scbond_other 4.073 r_mcangle_other 3.755 r_mcangle_it 3.753 r_mcbond_it 2.901 r_mcbond_other 2.891 r_chiral_restr_other 2.118 r_angle_refined_deg 1.705 r_angle_other_deg 1.546 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.198 r_symmetry_nbd_other 0.187 r_nbd_other 0.182 r_symmetry_xyhbond_nbd_other 0.169 r_symmetry_xyhbond_nbd_refined 0.157 r_nbtor_refined 0.156 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.011 r_xyhbond_nbd_other 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1960 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing