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Crystal structure of oxidized homoserine dehydrogenase of Sulfolobus tokodaii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 285 PEG 3350, magnesium chloride, PEG 400, DMSO
Crystal Properties Matthews coefficient Solvent content 2.16 43.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.818 α = 90 b = 78.909 β = 105.79 c = 65.814 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 2014-11-16 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) 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 1.6 50 99.2 0.078 38.8 4.6 74576
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 1.6 1.63 100 0.295 7.2 4.9
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 1.6 28.5 70670 3752 99.23 0.19811 0.19655 0.1967 0.22799 0.2282 RANDOM 24.553
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] 0.14 0.87 -0.97 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.328 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 12.236 r_dihedral_angle_1_deg 5.552 r_long_range_B_refined 4.73 r_mcangle_it 2.054 r_scbond_it 1.885 r_mcbond_it 1.304 r_angle_refined_deg 1.293 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.328 r_dihedral_angle_4_deg 14.204 r_dihedral_angle_3_deg 12.236 r_dihedral_angle_1_deg 5.552 r_long_range_B_refined 4.73 r_mcangle_it 2.054 r_scbond_it 1.885 r_mcbond_it 1.304 r_angle_refined_deg 1.293 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4576 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing