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Structure of beta-mannanase BaMan113A with mannobiose
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 2.89 57.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.493 α = 90 b = 110.284 β = 90 c = 150.438 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 S 6M 2018-10-19 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 1.65 25 97.9 0.858 11.8 7.4 108815
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 1.65 1.71 0.905
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 1.65 25 103293 5413 96.25 0.1665 0.1654 0.1717 0.1882 0.1947 RANDOM 21.568
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] -1.71 3.1 -1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.441 r_dihedral_angle_3_deg 14.67 r_dihedral_angle_4_deg 12.495 r_dihedral_angle_1_deg 7.472 r_angle_refined_deg 1.585 r_angle_other_deg 1.514 r_chiral_restr 0.116 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.441 r_dihedral_angle_3_deg 14.67 r_dihedral_angle_4_deg 12.495 r_dihedral_angle_1_deg 7.472 r_angle_refined_deg 1.585 r_angle_other_deg 1.514 r_chiral_restr 0.116 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5243 Nucleic Acid Atoms Solvent Atoms 764 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing