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Crystal structure of homoserine dehydrogenase in complex with L-cysteine and NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YDR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 PEG3350, di-ammonium tartrate
Crystal Properties Matthews coefficient Solvent content 2.4 48.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.171 α = 90 b = 106.171 β = 90 c = 56.874 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2016-06-22 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 Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.1 75.074 100 0.08 0.087 0.032 18.4 7.5 18629 18629
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.21 100 0.932 0.932 1 0.363 0.8 7.5 2709
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 4YDR 2.1 50.01 17691 931 99.97 0.1919 0.1896 0.1895 0.2394 0.2386 RANDOM 38.488
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] 0.57 0.57 -1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.077 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_4_deg 14.994 r_dihedral_angle_1_deg 5.978 r_angle_refined_deg 1.452 r_chiral_restr 0.147 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2286 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction XDS data reduction MOLREP phasing