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Crystal structure of the reduced form of homoserine dehydrogenase from Sulfolobus tokodaii.
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 PEG 2000, magnesium chloride, PEG 400, 1,4-butanediol
Crystal Properties Matthews coefficient Solvent content 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.401 α = 90 b = 79.472 β = 107.16 c = 65.899 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 95 PIXEL DECTRIS PILATUS 2M-F 2015-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 50 90.6 0.062 0.078 0.047 13.7 2.5 47593
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 1.8 1.83 94.8 0.261 0.328 0.196 0.911 2.4 2471
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 1.8 50 45154 2426 90.27 0.2129 0.2111 0.2197 0.247 0.216 RANDOM 31.185
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] 1.54 0.84 -0.72 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.721 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 5.621 r_mcangle_it 2.473 r_mcbond_it 1.608 r_mcbond_other 1.607 r_angle_refined_deg 1.245 r_angle_other_deg 0.738 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.721 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 13.494 r_dihedral_angle_1_deg 5.621 r_mcangle_it 2.473 r_mcbond_it 1.608 r_mcbond_other 1.607 r_angle_refined_deg 1.245 r_angle_other_deg 0.738 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4500 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing