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Crystal Structure of Human Thioesterase Superfamily Member 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WN3 pdb entry 1WN3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 20 % PEG 3350, 0.2M Na/K phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.05 α = 90 b = 90.97 β = 90 c = 114.4 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 MARRESEARCH Mirrors 2006-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976 ESRF BM14
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 2.2 100 99.6 0.078 17.58 7.2 30948 30821 -3 34.6
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 2.4 99.8 0.28 7.5 7.3 6965
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1WN3 2.2 19.55 2 30894 29216 1538 99.55 0.21969 0.21698 0.27189 0.2739 RANDOM 17.43
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] -0.02 -0.06 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.82 r_dihedral_angle_4_deg 18.952 r_dihedral_angle_3_deg 18.149 r_dihedral_angle_1_deg 6.489 r_scangle_it 2.867 r_scbond_it 1.777 r_angle_refined_deg 1.591 r_mcangle_it 1.141 r_mcbond_it 0.742 r_symmetry_hbond_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.82 r_dihedral_angle_4_deg 18.952 r_dihedral_angle_3_deg 18.149 r_dihedral_angle_1_deg 6.489 r_scangle_it 2.867 r_scbond_it 1.777 r_angle_refined_deg 1.591 r_mcangle_it 1.141 r_mcbond_it 0.742 r_symmetry_hbond_refined 0.3 r_nbtor_refined 0.296 r_nbd_refined 0.235 r_symmetry_vdw_refined 0.226 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 3662 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection XDS data scaling MOLREP phasing