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Xylanase from Bacillus circulans mutant E78Q/F125A
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 291 22.5 %v/v PEGSB, 0.2 M LiSO4,
0.05 M Zn Acet, 0.1 M BIS-TRIS pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.51 51.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.714 α = 90 b = 78.714 β = 90 c = 131.998 γ = 90
Symmetry Space Group I 41 2 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 1.7 42.58 99.4 0.999 11.7 1.9 23035
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 1.7 1.73 0.655
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.7 42.58 21750 1091 98.32 0.19164 0.19053 0.1906 0.2138 0.2155 RANDOM 20.918
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] 0.63 0.63 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.674 r_dihedral_angle_1_deg 8.733 r_dihedral_angle_2_deg 6.274 r_long_range_B_refined 6.085 r_long_range_B_other 6.066 r_scangle_other 4.03 r_scbond_it 2.819 r_scbond_other 2.817 r_mcangle_other 1.999 r_mcangle_it 1.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 10.674 r_dihedral_angle_1_deg 8.733 r_dihedral_angle_2_deg 6.274 r_long_range_B_refined 6.085 r_long_range_B_other 6.066 r_scangle_other 4.03 r_scbond_it 2.819 r_scbond_other 2.817 r_mcangle_other 1.999 r_mcangle_it 1.998 r_mcbond_it 1.618 r_mcbond_other 1.618 r_angle_refined_deg 1.476 r_angle_other_deg 0.506 r_chiral_restr 0.069 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 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 1442 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing