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Crystal structure of carnitinyl-CoA hydratase from Mycobacterium avium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QXI PDB ENTRY 3QXI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 MyavA.01530.a.A1 PW29034 at 26.76 mg/mL against JCSG+ screen condition D12: 40 mM potassium phosphate monobasic, 15% PEG8000, 20% glycerol, crystal tracking ID 216675d12, pH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.63 53.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.89 α = 90 b = 105.61 β = 90 c = 109.52 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 RIGAKU SATURN 944+ VariMax 2010-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.1 50 97.7 0.073 12.78 3.3 54122 52876 -3 27.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 80.2 0.289 2.93 2 3967
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 PDB ENTRY 3QXI 2.1 50 52700 2665 97.39 0.1718 0.1694 0.174 0.2163 0.2209 RANDOM 21.3216
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] -2.04 0.67 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.674 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_1_deg 5.502 r_scangle_it 3.567 r_scbond_it 2.117 r_angle_refined_deg 1.327 r_mcangle_it 1.174 r_mcbond_it 0.641 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.674 r_dihedral_angle_4_deg 19.126 r_dihedral_angle_3_deg 13.479 r_dihedral_angle_1_deg 5.502 r_scangle_it 3.567 r_scbond_it 2.117 r_angle_refined_deg 1.327 r_mcangle_it 1.174 r_mcbond_it 0.641 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5733 Nucleic Acid Atoms Solvent Atoms 564 Heterogen Atoms 27
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection XDS data reduction