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Hyperthermophilic archaeal homoserine dehydrogenase in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 2-methyl-2,4-pentandiol, potassium phosphate
Crystal Properties Matthews coefficient Solvent content 4.35 71.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.56 α = 90 b = 112.56 β = 90 c = 95.885 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 100 CCD ADSC QUANTUM 270 2012-06-25 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 Sym 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 2.3 50 99.8 0.051 21.4 7.6 53097
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.9 0.285 9.1 7.5
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 3DO5 2.3 50 50089 2685 99.19 0.1705 0.1687 0.1793 0.2046 0.2133 RANDOM 46.494
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] 0.35 0.35 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.403 r_dihedral_angle_4_deg 20.562 r_dihedral_angle_3_deg 18.106 r_dihedral_angle_1_deg 6.843 r_mcangle_it 5.721 r_mcbond_it 4.166 r_mcbond_other 4.165 r_angle_refined_deg 2.133 r_angle_other_deg 0.956 r_chiral_restr 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.403 r_dihedral_angle_4_deg 20.562 r_dihedral_angle_3_deg 18.106 r_dihedral_angle_1_deg 6.843 r_mcangle_it 5.721 r_mcbond_it 4.166 r_mcbond_other 4.165 r_angle_refined_deg 2.133 r_angle_other_deg 0.956 r_chiral_restr 0.135 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4916 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 138
Software Software Software Name Purpose HKL-2000 data reduction DM refinement REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling MOLREP phasing