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Crystal structure of prephenate dehydrogenase from A. aeolicus with HPP and NADH
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 100mM HEPES, 48% MPD, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.496 α = 90 b = 92.481 β = 90 c = 164.083 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 2.15 46.24 96.4 0.048 47.3 9.1 66487 1.3
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 2.15 2.19 67.5 0.52 1.3 4.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2G5C 2.15 46.22 66783 64377 2030 96.29 0.2189 0.21755 0.262 0.2998 RANDOM 38.906
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] 0.62 -0.18 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.644 r_dihedral_angle_4_deg 19.858 r_dihedral_angle_3_deg 19.114 r_dihedral_angle_1_deg 6.494 r_scangle_it 3.936 r_scbond_it 2.67 r_angle_refined_deg 1.804 r_mcangle_it 1.502 r_mcbond_it 0.883 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.644 r_dihedral_angle_4_deg 19.858 r_dihedral_angle_3_deg 19.114 r_dihedral_angle_1_deg 6.494 r_scangle_it 3.936 r_scbond_it 2.67 r_angle_refined_deg 1.804 r_mcangle_it 1.502 r_mcbond_it 0.883 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.213 r_xyhbond_nbd_refined 0.155 r_symmetry_vdw_refined 0.15 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 8922 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 202
Software Software Software Name Purpose HKL-3000 data collection AMoRE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling