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A new crystal structure of a Fusarium oxysporum GH10 xylanase reveals the presence of an extended loop on top of the catalytic cleft
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CUI PDB ENTRY 3CUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 17% PEG 10000, 0.1 M ammonium acetate, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.02 59.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.22 α = 90 b = 124.22 β = 90 c = 284.04 γ = 90
Symmetry Space Group P 41 21 2
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 MAR CCD 165 mm 2009-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 17.9 173419
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 3CUI 1.94 17.91 154871 8169 99.48 0.2142 0.21274 0.212 0.24183 0.2403 RANDOM 16.344
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] 0.03 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_dihedral_angle_4_deg 16.636 r_dihedral_angle_3_deg 12.142 r_dihedral_angle_1_deg 6.005 r_scangle_it 1.708 r_angle_refined_deg 1.069 r_scbond_it 1.057 r_mcangle_it 0.638 r_mcbond_it 0.33 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.741 r_dihedral_angle_4_deg 16.636 r_dihedral_angle_3_deg 12.142 r_dihedral_angle_1_deg 6.005 r_scangle_it 1.708 r_angle_refined_deg 1.069 r_scbond_it 1.057 r_mcangle_it 0.638 r_mcbond_it 0.33 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 12702 Nucleic Acid Atoms Solvent Atoms 1901 Heterogen Atoms 343
Software Software Software Name Purpose DNA data collection BALBES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling