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Structural insights into the acidophilic pH adaptation of a novel endo-1,4-beta-xylanase from Scytalidium acidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BK1 PDB ENTRY 1BK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 298 2M ammonium sulphate, 100mM CAPS (pH 10.5) and 200mM sulphate lithium, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.89 57.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.66 α = 90 b = 144.66 β = 90 c = 144.66 γ = 90
Symmetry Space Group P 21 3
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 2007-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.9797 ESRF BM30A
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 1.89 20 99.5 0.034 35.6 80178 2 2
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) 1.89 2 99.1 0.135 9.49
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1BK1 1.89 5.99 74004 3908 100 0.16831 0.16679 0.1664 0.19738 0.1971 RANDOM 26.348
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 14.288 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 7.756 r_scangle_it 2.634 r_scbond_it 2.001 r_angle_refined_deg 1.406 r_mcangle_it 1.294 r_mcbond_it 0.758 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.748 r_dihedral_angle_4_deg 14.288 r_dihedral_angle_3_deg 11.847 r_dihedral_angle_1_deg 7.756 r_scangle_it 2.634 r_scbond_it 2.001 r_angle_refined_deg 1.406 r_mcangle_it 1.294 r_mcbond_it 0.758 r_nbtor_refined 0.305 r_xyhbond_nbd_refined 0.256 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.138 r_symmetry_hbond_refined 0.13 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 5472 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 70
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement XDS data reduction XSCALE data scaling