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STRUCTURE OF D-2-HYDROXYISOCAPROATE DEHYDROGENASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GDH BACKBONE AND C-BETA ATOMS OF D-GLYCERATE DEHYDROGENASE (PDB ENTRY 1GDH)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 277 1.9 M AMMONIUM SULFATE, 50 MM CITRATE/PHOSPHATE BUFFER, 30 MM NAD+, 60 MM 4-METHYL-2-OXOPENTANOATE, PH 7.0, 277 K; ENZYME CONCENTRATION 10 MG/ML.
Crystal Properties Matthews coefficient Solvent content 4.4 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.1 α = 90 b = 134.1 β = 90 c = 125.1 γ = 120
Symmetry Space Group P 63 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE MAR scanner 300 mm plate MIRROR OPTICS 1994-08-01 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MPG/DESY, HAMBURG BEAMLINE BW6 MPG/DESY, HAMBURG BW6
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 1.86 12.1 96.5 0.089 22.2 5.8 53838
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 1.86 2 86.9 0.48 2.8 4.4
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT BACKBONE AND C-BETA ATOMS OF D-GLYCERATE DEHYDROGENASE (PDB ENTRY 1GDH) 1.86 12.1 53838 96.5 0.196 0.196 0.1955 0.217 31.02
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]
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.12 x_angle_deg 1.73 x_improper_angle_d 1.25 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation x_dihedral_angle_d 23.12 x_angle_deg 1.73 x_improper_angle_d 1.25 x_bond_d 0.009 x_bond_d_na x_bond_d_prot x_angle_d x_angle_d_na x_angle_d_prot x_angle_deg_na x_angle_deg_prot x_dihedral_angle_d_na x_dihedral_angle_d_prot x_improper_angle_d_na x_improper_angle_d_prot x_mcbond_it x_mcangle_it x_scbond_it x_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2580 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 63
Software Software Software Name Purpose X-PLOR model building X-PLOR refinement MOSFLM data reduction CCP4 data scaling ROTAVATA data scaling X-PLOR phasing