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Crystal structure of Homoserine dehydrogenase (NP_394635.1) from THERMOPLASMA ACIDOPHILUM at 1.95 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.14 293 49.0000% 2-propanol, 5.0000% polyethylene glycol 1000, 0.1M citric acid pH 5.14, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.69 54.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.821 α = 90 b = 92.113 β = 90 c = 120.788 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-03-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97927,0.97908 SSRL BL9-2
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 1.95 28.105 98.6 0.079 8.45 3.65 28686 -3 20.319
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 1.95 2.02 97.2 0.499 1.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.95 28.105 28657 1435 99.6 0.154 0.152 0.193 0.1806 RANDOM 28.208
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] 0.05 0.99 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.7 r_dihedral_angle_4_deg 15.33 r_dihedral_angle_3_deg 11.692 r_scangle_it 7.159 r_dihedral_angle_1_deg 5.14 r_scbond_it 4.977 r_mcangle_it 3.113 r_mcbond_it 1.909 r_angle_refined_deg 1.623 r_angle_other_deg 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.7 r_dihedral_angle_4_deg 15.33 r_dihedral_angle_3_deg 11.692 r_scangle_it 7.159 r_dihedral_angle_1_deg 5.14 r_scbond_it 4.977 r_mcangle_it 3.113 r_mcbond_it 1.909 r_angle_refined_deg 1.623 r_angle_other_deg 1.12 r_mcbond_other 0.543 r_symmetry_vdw_other 0.311 r_nbd_refined 0.242 r_symmetry_vdw_refined 0.238 r_symmetry_hbond_refined 0.224 r_nbd_other 0.197 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.182 r_nbtor_other 0.091 r_chiral_restr 0.078 r_xyhbond_nbd_other 0.027 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2405 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 73
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SHARP phasing