☰ Navigation Tabs
Crystal structure of Acetyl xylan esterase (TM0077) from THERMOTOGA MARITIMA at 2.50 A resolution (native apo 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, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.46 α = 90 b = 103.79 β = 90 c = 221.02 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 2.5 48.795 100 0.207 14.37 83045 -3 44.247
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 2.5 2.56 100 0.011 2.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MR THROUGHOUT 1vlq 2.5 48.795 83045 4200 99.99 0.169 0.167 0.212 0.1798 RANDOM 29.065
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] -0.68 0.24 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.496 r_dihedral_angle_4_deg 17.772 r_dihedral_angle_3_deg 14.952 r_scangle_it 5.97 r_dihedral_angle_1_deg 5.954 r_scbond_it 4.698 r_mcangle_it 2.577 r_mcbond_it 1.748 r_angle_refined_deg 1.469 r_angle_other_deg 0.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.496 r_dihedral_angle_4_deg 17.772 r_dihedral_angle_3_deg 14.952 r_scangle_it 5.97 r_dihedral_angle_1_deg 5.954 r_scbond_it 4.698 r_mcangle_it 2.577 r_mcbond_it 1.748 r_angle_refined_deg 1.469 r_angle_other_deg 0.972 r_symmetry_vdw_other 0.322 r_symmetry_vdw_refined 0.285 r_nbd_refined 0.218 r_mcbond_other 0.217 r_nbd_other 0.197 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.148 r_metal_ion_refined 0.124 r_symmetry_hbond_refined 0.101 r_chiral_restr 0.088 r_nbtor_other 0.088 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 15568 Nucleic Acid Atoms Solvent Atoms 507 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PHASER phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction