☰ Navigation Tabs
Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.40 A resolution (PMSF 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 phenylmethylsulfonyl fluoride (PMSF), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.57 α = 90 b = 104.5 β = 90 c = 221.61 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 2.4 48.97 100 0.18 11.5 94681 -3 34.88
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 2.4 2.46 100 0.674 3.4
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 2.4 48.97 94680 4742 99.99 0.162 0.16 0.1639 0.208 0.2089 RANDOM 23.244
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] -1.32 0.12 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.775 r_dihedral_angle_4_deg 16.887 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_1_deg 6.38 r_scangle_it 5.807 r_scbond_it 4.646 r_mcangle_it 2.593 r_mcbond_it 1.803 r_angle_refined_deg 1.532 r_angle_other_deg 1.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.775 r_dihedral_angle_4_deg 16.887 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_1_deg 6.38 r_scangle_it 5.807 r_scbond_it 4.646 r_mcangle_it 2.593 r_mcbond_it 1.803 r_angle_refined_deg 1.532 r_angle_other_deg 1.018 r_symmetry_vdw_other 0.301 r_symmetry_vdw_refined 0.268 r_mcbond_other 0.26 r_symmetry_hbond_refined 0.213 r_nbd_refined 0.199 r_nbd_other 0.194 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_other 0.124 r_metal_ion_refined 0.099 r_chiral_restr 0.088 r_nbtor_other 0.086 r_bond_refined_d 0.017 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 15616 Nucleic Acid Atoms Solvent Atoms 946 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PHASER phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction