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Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.12 A resolution (paraoxon inhibitor complex structure)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 277 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, Additive: 0.004 M diethyl p-nitrophenyl phosphate (paraoxon), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.58 52.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.797 α = 90 b = 104.431 β = 90 c = 221.644 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 ADSC QUANTUM 315 2009-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 2.12 48.97 89.8 0.095 15.26 123070 -3 26.92
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 2.12 2.18 53.5 0.519 2.2
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 MR THROUGHOUT 1vlq 2.12 48.97 122994 6188 89.82 0.169 0.168 0.1715 0.205 0.207 RANDOM 23.858
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] -0.73 -0.1 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.659 r_dihedral_angle_4_deg 16.767 r_dihedral_angle_3_deg 13.989 r_dihedral_angle_1_deg 6.201 r_scangle_it 5.792 r_scbond_it 4.446 r_mcangle_it 2.523 r_mcbond_it 1.775 r_angle_refined_deg 1.437 r_angle_other_deg 0.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.659 r_dihedral_angle_4_deg 16.767 r_dihedral_angle_3_deg 13.989 r_dihedral_angle_1_deg 6.201 r_scangle_it 5.792 r_scbond_it 4.446 r_mcangle_it 2.523 r_mcbond_it 1.775 r_angle_refined_deg 1.437 r_angle_other_deg 0.983 r_symmetry_vdw_refined 0.314 r_mcbond_other 0.283 r_symmetry_vdw_other 0.257 r_nbd_refined 0.198 r_nbd_other 0.191 r_xyhbond_nbd_other 0.184 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.086 r_nbtor_other 0.086 r_metal_ion_refined 0.08 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15755 Nucleic Acid Atoms Solvent Atoms 985 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PHASER phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction