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High resolution apo structure of isomerase PaaG
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 2.07 40.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.497 α = 90 b = 88.497 β = 90 c = 88.497 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 1.27 44.25 95 0.997 23.38 9.1 58055
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 1.27 1.316 0.4146
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3HRX 1.27 44.25 55201 2861 95.003 0.147 0.1457 0.1788 0.1778 16.898
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 26.393 r_dihedral_angle_4_deg 16.584 r_dihedral_angle_3_deg 12.699 r_dihedral_angle_1_deg 6.087 r_lrange_it 4.892 r_scangle_it 4.788 r_scangle_other 4.787 r_lrange_other 4.782 r_rigid_bond_restr 4.314 r_scbond_it 4.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.393 r_dihedral_angle_4_deg 16.584 r_dihedral_angle_3_deg 12.699 r_dihedral_angle_1_deg 6.087 r_lrange_it 4.892 r_scangle_it 4.788 r_scangle_other 4.787 r_lrange_other 4.782 r_rigid_bond_restr 4.314 r_scbond_it 4.084 r_scbond_other 4.083 r_mcangle_it 2.893 r_mcangle_other 2.892 r_mcbond_it 2.355 r_mcbond_other 2.351 r_angle_refined_deg 1.942 r_angle_other_deg 1.654 r_nbd_refined 0.24 r_symmetry_nbd_refined 0.218 r_nbd_other 0.195 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.175 r_chiral_restr 0.126 r_xyhbond_nbd_refined 0.121 r_symmetry_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1967 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing