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Structure of D-amino acid dehydrogenase in complex with NADPH and 2-keto-6-aminocapronic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GZ1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.51 51.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.838 α = 90 b = 94.773 β = 90 c = 138.791 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 ADSC QUANTUM 270 silicon single crystal 2015-12-04 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) 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 1.74 50 99.8 0.116 9.2 7 74999
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 100 1.617 0.411 7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5GZ1 1.74 50 71112 3780 99.64 0.2097 0.2075 0.2219 0.2502 0.2525 RANDOM 35.261
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] -0.07 0.8 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.377 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 14.152 r_dihedral_angle_1_deg 6.784 r_mcangle_it 3.892 r_mcbond_it 2.578 r_mcbond_other 2.578 r_angle_refined_deg 2.357 r_angle_other_deg 1.215 r_chiral_restr 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.377 r_dihedral_angle_4_deg 16.775 r_dihedral_angle_3_deg 14.152 r_dihedral_angle_1_deg 6.784 r_mcangle_it 3.892 r_mcbond_it 2.578 r_mcbond_other 2.578 r_angle_refined_deg 2.357 r_angle_other_deg 1.215 r_chiral_restr 0.156 r_bond_refined_d 0.028 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4920 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 72
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing