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The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CIV PDB ENTRY 3CIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.1 M SODIUM ACETATE PH 4.6, 4% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.17 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.92 α = 90 b = 76.16 β = 90 c = 93.73 γ = 90
Symmetry Space Group P 21 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 PILATUS 6M MIRRORS 2013-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.64 46.87 99.4 0.07 12.7 6.3 39738 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.64 1.69 99.1 0.61 2.5 5.7
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 3CIV 1.64 46.87 37678 1995 99.34 0.14651 0.14345 0.1571 0.20828 0.2199 RANDOM 32.018
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] 2.9 -4.02 1.12
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.347 r_dihedral_angle_2_deg 30.972 r_dihedral_angle_4_deg 18.589 r_sphericity_bonded 17.397 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 5.816 r_scangle_it 5.423 r_mcangle_it 4.513 r_scbond_it 4.491 r_mcbond_it 3.875
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 34.347 r_dihedral_angle_2_deg 30.972 r_dihedral_angle_4_deg 18.589 r_sphericity_bonded 17.397 r_dihedral_angle_3_deg 13.514 r_dihedral_angle_1_deg 5.816 r_scangle_it 5.423 r_mcangle_it 4.513 r_scbond_it 4.491 r_mcbond_it 3.875 r_mcbond_other 3.873 r_rigid_bond_restr 3.285 r_angle_refined_deg 1.363 r_angle_other_deg 0.823 r_symmetry_vdw_refined 0.3 r_symmetry_vdw_other 0.251 r_nbd_refined 0.246 r_nbtor_refined 0.188 r_nbd_other 0.181 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.084 r_nbtor_other 0.083 r_symmetry_hbond_refined 0.023 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2466 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing