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Structure of amino acid dehydrogenase-2752 with ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2-propanol, PEG 4000, Hepes buffer, NAD, pyruvate
Crystal Properties Matthews coefficient Solvent content 3.66 66.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.601 α = 90 b = 194.601 β = 90 c = 158.472 γ = 120
Symmetry Space Group P 64 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 2016-11-23 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) 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 50 99.8 0.106 4.3 10.2 89460
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 97 0.736 8.5
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 2.2 49.69 84971 4494 99.83 0.18472 0.18256 0.1934 0.22535 0.2299 RANDOM 41.672
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] -1.12 -0.56 -1.12 3.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.124 r_dihedral_angle_4_deg 17.058 r_dihedral_angle_3_deg 14.144 r_long_range_B_refined 8.697 r_long_range_B_other 8.696 r_dihedral_angle_1_deg 7.377 r_scangle_other 6.907 r_mcangle_it 5.03 r_mcangle_other 5.03 r_scbond_it 4.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.124 r_dihedral_angle_4_deg 17.058 r_dihedral_angle_3_deg 14.144 r_long_range_B_refined 8.697 r_long_range_B_other 8.696 r_dihedral_angle_1_deg 7.377 r_scangle_other 6.907 r_mcangle_it 5.03 r_mcangle_other 5.03 r_scbond_it 4.889 r_scbond_other 4.889 r_mcbond_it 3.602 r_mcbond_other 3.59 r_angle_refined_deg 1.815 r_angle_other_deg 1.376 r_chiral_restr 0.079 r_bond_refined_d 0.011 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8229 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing