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Crystal structure of a glutamate-1-semialdehyde-aminomutase (K286A) from Pseudomonas aeruginosa PAO1 in complex with PMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1M Tris pH 6.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.15 42.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.73 α = 90 b = 97.104 β = 90 c = 100.52 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2016-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9786 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.57 50 99.6 32.6 6.5 121760
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5YKR 1.57 50 119684 1998 99.41 0.15437 0.15393 0.1638 0.18004 0.1897 RANDOM 25.237
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] 1.33 -0.82 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.798 r_dihedral_angle_4_deg 15.024 r_dihedral_angle_3_deg 12.233 r_long_range_B_refined 9.215 r_long_range_B_other 9.208 r_scangle_other 8.656 r_scbond_it 6.974 r_scbond_other 6.966 r_dihedral_angle_1_deg 6.101 r_mcangle_it 2.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.798 r_dihedral_angle_4_deg 15.024 r_dihedral_angle_3_deg 12.233 r_long_range_B_refined 9.215 r_long_range_B_other 9.208 r_scangle_other 8.656 r_scbond_it 6.974 r_scbond_other 6.966 r_dihedral_angle_1_deg 6.101 r_mcangle_it 2.861 r_mcangle_other 2.86 r_mcbond_it 2.365 r_mcbond_other 2.364 r_angle_refined_deg 1.353 r_angle_other_deg 0.958 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7048 Nucleic Acid Atoms Solvent Atoms 832 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing