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The crystal structure of A. aeolicus prephenate dehydrogenase in complex with tyrosine and NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G5C pdb entry 2g5c
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 298 48% MPD, 100 mM HEPES, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.16 43.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.431 α = 90 b = 93.691 β = 90 c = 163.656 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 SBC-2 2007-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 46.85 99.1 0.07 40 8.9 62250 61690 2.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.262 93.1 0.311 2.5 6.8
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 2g5c 2.21 46.85 59735 59708 1913 98.86 0.1948 0.19291 0.1995 0.25419 0.2514 RANDOM 16.613
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] -0.12 -0.12 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.128 r_dihedral_angle_4_deg 20.932 r_dihedral_angle_3_deg 19.008 r_dihedral_angle_1_deg 6.616 r_scangle_it 4.64 r_scbond_it 3.037 r_angle_refined_deg 1.992 r_mcangle_it 1.673 r_mcbond_it 0.943 r_chiral_restr 0.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.128 r_dihedral_angle_4_deg 20.932 r_dihedral_angle_3_deg 19.008 r_dihedral_angle_1_deg 6.616 r_scangle_it 4.64 r_scbond_it 3.037 r_angle_refined_deg 1.992 r_mcangle_it 1.673 r_mcbond_it 0.943 r_chiral_restr 0.142 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9062 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 200
Software Software Software Name Purpose HKL-3000 data collection AMoRE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling