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2.15 Angstroms X-ray crystal structure of NAD- and alternative substrate-bound 2-aminomuconate 6-semialdehyde dehydrogenase 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 3,350
, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.566 α = 90 b = 142.724 β = 90 c = 175.006 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 300 mm CCD 2012-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.8 APS 22-ID
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 2.15 45 99.9 0.122 12.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.19 100
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 2.15 27.47 149355 114123 6029 99.68 0.18258 0.17971 0.1874 0.23671 0.2386 RANDOM 39.811
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] -2.22 -1.47 3.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.644 r_dihedral_angle_4_deg 21.605 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.481 r_angle_refined_deg 1.798 r_angle_other_deg 0.871 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.644 r_dihedral_angle_4_deg 21.605 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.481 r_angle_refined_deg 1.798 r_angle_other_deg 0.871 r_chiral_restr 0.105 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scbond_it 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 14684 Nucleic Acid Atoms Solvent Atoms 799 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing PHENIX refinement