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Structure of D-amino acid dehydrogenase in complex with NADP
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 7 293 PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.585 α = 90 b = 78.232 β = 107.25 c = 68.969 γ = 90
Symmetry Space Group P 1 21 1
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 1.59 50 93.7 0.084 16 6.3 81038
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 1.59 1.62 83.1 0.458 0.84 5.6
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 1.59 50 76871 4071 93.56 0.1933 0.1914 0.211 0.2293 0.236 RANDOM 20.81
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] 1.69 1.36 -1.68 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.013 r_dihedral_angle_4_deg 17.995 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 6.739 r_angle_refined_deg 2.621 r_mcangle_it 1.987 r_mcbond_it 1.407 r_mcbond_other 1.407 r_angle_other_deg 1.241 r_chiral_restr 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.013 r_dihedral_angle_4_deg 17.995 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 6.739 r_angle_refined_deg 2.621 r_mcangle_it 1.987 r_mcbond_it 1.407 r_mcbond_other 1.407 r_angle_other_deg 1.241 r_chiral_restr 0.174 r_bond_refined_d 0.03 r_gen_planes_refined 0.016 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4983 Nucleic Acid Atoms Solvent Atoms 370 Heterogen Atoms 112
Software Software Software Name Purpose HKL-2000 data collection HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing HKL-2000 data reduction