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Crystal structure of a haloacid dehalogenase-like hydrolase (Target EFI-900331) from Bacteroides thetaiotaomicron with bound Mg crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NIW PDB ENTRY 3NIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.75 298 protein solution: 10 mM HEPES, pH 7.8, 150 mM sodium chloride, 10% glycerol, 5 mM magnesium, reservoir solution: 20% PEG3350, 100 mM Bis-Tris, pH 5.5, 3% TMAO, cryoprotectant: reservoir solution + 20% glycerol + 50 mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.88 34.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.696 α = 90 b = 68.178 β = 90 c = 96.645 γ = 90
Symmetry Space Group P 21 21 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 RAYONIX MX225HE mirrors 2011-01-01 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 50 99.7 0.064 0.064 17.2 7 38562 38562 17.01
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 0.787 0.787 2.8 6.6 5559
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 PDB ENTRY 3NIW 1.5 24.161 38477 38477 1930 99.62 0.1781 0.1781 0.1769 0.1744 0.2018 0.2004 RANDOM 23.6186
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] -2.7538 4.9618 -1.9575
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.878 f_angle_d 1.616 f_chiral_restr 0.106 f_bond_d 0.016 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2092 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 7
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SCALA data scaling PHENIX phasing