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Crystal structure of D-mannonate dehydratase homolog from Chromohalobacter salexigens (Target EFI-502114), with bound NA, ordered loop
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BSM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 Protein (10 mM Hepes pH 7.5, 150 mM NaCl, 10% glycerol, 1 mM DTT, 5 mM MgCl), Reservoir (0.2 M NaAcetate, 0.1 M Tris-HCl pH 8.5, 30% Peg4000); Cryoprotection (Reservoir, + 20% glycerol), sitting drop vapor diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.74 55.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.389 α = 90 b = 111.389 β = 90 c = 84.576 γ = 90
Symmetry Space Group P 4 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 100 CCD RAYONIX MX225HE MIRRORS 2012-03-03 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 1.8 50 100 0.12 0.12 15.3 49800 49800 21.41
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 1.8 1.9 100 0.752 0.752 4.2 14.7 7150
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3BSM 1.8 30.894 1.34 49792 49792 2523 99.94 0.1459 0.1446 0.1441 0.1706 0.1679 RANDOM 27.7543
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] -3.6355 -3.6355 7.271
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.071 f_angle_d 1.052 f_chiral_restr 0.074 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3236 Nucleic Acid Atoms Solvent Atoms 343 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHENIX phasing