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Structure of amino acid dehydrogenase3448
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HYE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 293 iron (III) chloride, Jeffamine M-600, sodium citrate buffer, NAD, pyruvate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.621 α = 90 b = 149.621 β = 90 c = 137.394 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS 2M 2021-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.39 49.02 100 0.154 0.158 0.035 0.999 21.1 19.7 36433
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.48 99.9 1.677 1.724 0.397 0.714 18.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.39 48.97 34633 1778 99.91 0.18517 0.18381 0.1953 0.21121 0.2139 RANDOM 49.986
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] 0.66 0.33 0.66 -2.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.004 r_dihedral_angle_4_deg 22.149 r_dihedral_angle_3_deg 16.842 r_long_range_B_other 10.358 r_long_range_B_refined 10.352 r_scangle_other 9.211 r_dihedral_angle_1_deg 7.707 r_mcangle_it 6.581 r_mcangle_other 6.56 r_scbond_it 6.523
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.004 r_dihedral_angle_4_deg 22.149 r_dihedral_angle_3_deg 16.842 r_long_range_B_other 10.358 r_long_range_B_refined 10.352 r_scangle_other 9.211 r_dihedral_angle_1_deg 7.707 r_mcangle_it 6.581 r_mcangle_other 6.56 r_scbond_it 6.523 r_scbond_other 6.463 r_mcbond_it 4.942 r_mcbond_other 4.926 r_angle_refined_deg 1.894 r_angle_other_deg 1.453 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2717 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing