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Crystal structure of N-terminal domain of yeast peroxisomal thioesterase-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294 1.5 M sodium formate, 0.1 M sodium citrate buffer, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.84 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.261 α = 90 b = 80.261 β = 90 c = 137.079 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC QUANTUM 4 mirrors 2001-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X9B 0.9149 NSLS X9B
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 2.2 40 0.058 21.9 4.2 26378 -3
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) 2.2 2.26 99.8 0.225 2.8 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 2.2 12 25524 25524 852 100 0.21609 0.21609 0.21461 0.2603 0.2444 RANDOM 36.155
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] -0.21 -0.11 -0.21 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.51 r_scangle_it 4.26 r_scbond_it 2.568 r_mcangle_it 2.282 r_angle_refined_deg 1.835 r_mcbond_it 1.243 r_angle_other_deg 0.946 r_nbd_refined 0.271 r_nbd_other 0.26 r_xyhbond_nbd_refined 0.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 9.51 r_scangle_it 4.26 r_scbond_it 2.568 r_mcangle_it 2.282 r_angle_refined_deg 1.835 r_mcbond_it 1.243 r_angle_other_deg 0.946 r_nbd_refined 0.271 r_nbd_other 0.26 r_xyhbond_nbd_refined 0.206 r_symmetry_vdw_other 0.201 r_symmetry_vdw_refined 0.169 r_chiral_restr 0.12 r_nbtor_other 0.096 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.01 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_refined r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3101 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling SHELXD phasing SHARP phasing REFMAC refinement HKL-2000 data reduction