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Structure of amino acid dehydrogenase in complex with NADP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 PEG 8000, imidazole buffer, NaCl, NADP, lysine
Crystal Properties Matthews coefficient Solvent content 2.37 48.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.965 α = 90 b = 92.617 β = 90 c = 162.475 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 PIXEL DECTRIS PILATUS3 6M 2022-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.2 46.8 100 0.072 0.078 0.03 0.992 16.8 6.7 70419
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 2.2 2.25 100 1.192 1.288 0.487 0.73 7
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 2.2 46.8 66780 3563 99.99 0.21534 0.21296 0.2192 0.25957 0.2646 RANDOM 48.631
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] -2.32 0.06 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.379 r_long_range_B_other 8.442 r_long_range_B_refined 8.439 r_dihedral_angle_1_deg 7.119 r_dihedral_angle_2_deg 6.891 r_scangle_other 6.174 r_mcangle_it 5.471 r_mcangle_other 5.47 r_scbond_it 4.147 r_scbond_other 4.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.379 r_long_range_B_other 8.442 r_long_range_B_refined 8.439 r_dihedral_angle_1_deg 7.119 r_dihedral_angle_2_deg 6.891 r_scangle_other 6.174 r_mcangle_it 5.471 r_mcangle_other 5.47 r_scbond_it 4.147 r_scbond_other 4.146 r_mcbond_it 3.805 r_mcbond_other 3.8 r_angle_refined_deg 1.379 r_angle_other_deg 0.458 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 9119 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction MOLREP phasing