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Crystal structure of isomerase PaaG mutant - D136N with Oxepin-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 2.19 43.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.156 α = 90 b = 73.05 β = 92.482 c = 130.304 γ = 90
Symmetry Space Group P 1 21 1
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 2018-09-22 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 2.55 48.645 96.84 0.997 9.82 6.8 45527
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.641 0.2727
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 2.55 48.645 45463 2301 96.849 0.203 0.2008 0.2004 0.2523 0.2526 54.132
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] 1.753 0.423 0.459 -2.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.865 r_dihedral_angle_4_deg 21.395 r_dihedral_angle_3_deg 18.276 r_lrange_it 11.723 r_scangle_it 9.304 r_mcangle_it 7.253 r_scbond_it 6.69 r_dihedral_angle_1_deg 6.593 r_mcbond_it 5.149 r_angle_refined_deg 1.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.865 r_dihedral_angle_4_deg 21.395 r_dihedral_angle_3_deg 18.276 r_lrange_it 11.723 r_scangle_it 9.304 r_mcangle_it 7.253 r_scbond_it 6.69 r_dihedral_angle_1_deg 6.593 r_mcbond_it 5.149 r_angle_refined_deg 1.585 r_nbtor_refined 0.308 r_symmetry_nbd_refined 0.29 r_symmetry_xyhbond_nbd_refined 0.263 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.121 r_ncsr_local_group_1 0.099 r_ncsr_local_group_2 0.098 r_ncsr_local_group_15 0.096 r_ncsr_local_group_4 0.094 r_ncsr_local_group_9 0.094 r_ncsr_local_group_12 0.094 r_ncsr_local_group_11 0.093 r_ncsr_local_group_3 0.092 r_ncsr_local_group_6 0.092 r_ncsr_local_group_14 0.092 r_ncsr_local_group_8 0.09 r_ncsr_local_group_10 0.09 r_ncsr_local_group_13 0.088 r_ncsr_local_group_7 0.085 r_ncsr_local_group_5 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11166 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 348
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing