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Xylanase from Bacillus circulans mutant E78Q/Y69A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 10 %v/v PEGSB, 0.2 M LiSO4, BIS-TRIS, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.58 52.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.345 α = 90 b = 79.345 β = 90 c = 133.171 γ = 90
Symmetry Space Group P 43 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 PIXEL DECTRIS PILATUS 2M 2021-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.5 68.26 100 0.999 13.2 1.9 68694
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 0.849
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.5 68.26 65327 3356 99.98 0.15522 0.15379 0.1832 0.1832 RANDOM 19.116
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] 1.05 1.05 -2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 8.353 r_dihedral_angle_2_deg 6.921 r_long_range_B_refined 5.186 r_long_range_B_other 4.988 r_scangle_other 4.128 r_scbond_it 3.213 r_scbond_other 3.212 r_mcangle_it 2.584 r_mcangle_other 2.584
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.555 r_dihedral_angle_1_deg 8.353 r_dihedral_angle_2_deg 6.921 r_long_range_B_refined 5.186 r_long_range_B_other 4.988 r_scangle_other 4.128 r_scbond_it 3.213 r_scbond_other 3.212 r_mcangle_it 2.584 r_mcangle_other 2.584 r_mcbond_it 1.814 r_mcbond_other 1.813 r_angle_refined_deg 1.558 r_angle_other_deg 0.535 r_chiral_restr 0.072 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2882 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing