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A 2.20 angstroms X-ray crystal structure of E268A 2-aminomucaonate 6-semialdehyde dehydrogenase catalytic intermediate from Pseudomonas fluorescens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I1W pdb entry 4I1W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.1 291 0.2 M sodium phosphate dibasic dihydrate, 20% w/v polyethylene glycol 3350, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.6 52.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.329 α = 90 b = 141.345 β = 90 c = 173.53 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 CCD MARMOSAIC 225 mm CCD 2014-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 50 99.6 0.099 9.1 11.4 110998 110554
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 2.2 2.24 99.2 0.717 10.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 4I1W 2.19 41 111788 104815 5043 98.68 0.18242 0.18019 0.1756 0.22517 0.2161 RANDOM 36.1
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] -0.97 -0.97 1.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.213 r_dihedral_angle_4_deg 19.38 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 6.185 r_angle_other_deg 2.976 r_angle_refined_deg 1.666 r_bond_other_d 1.384 r_chiral_restr 0.146 r_bond_refined_d 0.018 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.213 r_dihedral_angle_4_deg 19.38 r_dihedral_angle_3_deg 14.575 r_dihedral_angle_1_deg 6.185 r_angle_other_deg 2.976 r_angle_refined_deg 1.666 r_bond_other_d 1.384 r_chiral_restr 0.146 r_bond_refined_d 0.018 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14668 Nucleic Acid Atoms Solvent Atoms 882 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction MAR345 data collection DENZO data reduction PHENIX phasing SCALEPACK data scaling