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Crystal structure of a short chain dehydrogenase homolog (target efi-505321) from burkholderia multivorans, unliganded structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 sitting drop vapor diffusion 7.5 298 Protein (50 mM Hepes pH 7.5; Reservoir (0.2 M Calcium Acetate 0.1 M HEPES:NaOH pH 7.5 10% (w/v) PEG 8000); Cryoprotection (Reservoir, + 20% Ethylene glycol), sitting drop vapor diffusion, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.96 α = 90 b = 99.96 β = 90 c = 205.801 γ = 120
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 RAYONIX MX-225 MIRRORS 2012-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 86.567 100 0.11 0.11 10.8 8.9 185302 185302
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 100 0.836 0.836 0.9 9.3 27085
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1YDE 1.5 22.873 185136 185136 9297 99.97 0.1524 0.1524 0.1513 0.1512 0.1719 0.1703 RANDOM 15.9898
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 f_dihedral_angle_d 13.834 f_angle_d 1.087 f_chiral_restr 0.076 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7639 Nucleic Acid Atoms Solvent Atoms 1070 Heterogen Atoms 21
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing