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Structure of a novel beta-mannanase BaMan113A with mannobiose, N236Y mutation.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.85 56.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.194 α = 90 b = 109.375 β = 90 c = 150.504 γ = 90
Symmetry Space Group P 2 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 PIXEL DECTRIS PILATUS3 6M 2019-10-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.979 SSRF BL19U1
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 1.9 25 93.5 0.871 16.5 11.9 68892
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 1.9 1.97 0.932
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 3CIV 1.9 25 65225 3600 93.15 0.1626 0.1607 0.1742 0.1972 0.2101 RANDOM 22.3
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] -0.99 2.22 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.631 r_dihedral_angle_4_deg 17.461 r_dihedral_angle_3_deg 14.145 r_dihedral_angle_1_deg 7.336 r_angle_refined_deg 1.653 r_angle_other_deg 1.469 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.631 r_dihedral_angle_4_deg 17.461 r_dihedral_angle_3_deg 14.145 r_dihedral_angle_1_deg 7.336 r_angle_refined_deg 1.653 r_angle_other_deg 1.469 r_chiral_restr 0.123 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5283 Nucleic Acid Atoms Solvent Atoms 677 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing