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Crystal structure of acyl-coa thioesterase from mycobacterium avium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C8U pdb deposition 1c8u modified with ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 10MMM HEPES PH 7.0, 35% PEG 3350; MYAVA.00458.A.A1 PS00622 AT 60MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.34 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.75 α = 90 b = 62.8 β = 99.92 c = 82.22 γ = 90
Symmetry Space Group P 1 21 1
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+ 2010-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 1.95 50 99.1 0.06 0.06 22.15 6.3 42464 42081 -3 27.38
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 1.95 2 94.3 0.361 0.361 3.8 3.8 3135
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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 THROUGHOUT pdb deposition 1c8u modified with ccp4 program chainsaw 1.95 36.05 42464 42023 2152 99 0.166 0.166 0.164 0.1686 0.198 0.2046 RANDOM 17.86
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] 0.09 0.38 0.3 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.907 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 12.581 r_dihedral_angle_1_deg 5.946 r_scangle_it 3.474 r_scbond_it 2.212 r_mcangle_it 1.505 r_angle_refined_deg 1.464 r_angle_other_deg 0.877 r_mcbond_it 0.832
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.907 r_dihedral_angle_4_deg 16.409 r_dihedral_angle_3_deg 12.581 r_dihedral_angle_1_deg 5.946 r_scangle_it 3.474 r_scbond_it 2.212 r_mcangle_it 1.505 r_angle_refined_deg 1.464 r_angle_other_deg 0.877 r_mcbond_it 0.832 r_mcbond_other 0.215 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4185 Nucleic Acid Atoms Solvent Atoms 390 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling