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The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManIFG and beta-1,4-mannobiose
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 2.52 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.472 α = 90 b = 76.586 β = 90 c = 140.212 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 2013-05-26 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 1.65 76.59 97.9 0.16 6.7 6.3 88667 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 1.65 1.68 78.3 0.63 1.8 4.7
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 1.65 70.11 83793 4466 97.32 0.15313 0.15081 0.1657 0.19617 0.207 RANDOM 15.621
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] -0.4 0.6 -0.2
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.61 r_dihedral_angle_2_deg 28.686 r_dihedral_angle_4_deg 15.523 r_dihedral_angle_3_deg 12.606 r_sphericity_bonded 8.839 r_dihedral_angle_1_deg 6.118 r_scangle_it 3.341 r_scbond_it 2.773 r_rigid_bond_restr 2.466 r_mcangle_it 2.357
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.61 r_dihedral_angle_2_deg 28.686 r_dihedral_angle_4_deg 15.523 r_dihedral_angle_3_deg 12.606 r_sphericity_bonded 8.839 r_dihedral_angle_1_deg 6.118 r_scangle_it 3.341 r_scbond_it 2.773 r_rigid_bond_restr 2.466 r_mcangle_it 2.357 r_mcbond_it 1.975 r_mcbond_other 1.975 r_angle_refined_deg 1.405 r_angle_other_deg 1.03 r_symmetry_vdw_refined 0.344 r_nbd_refined 0.244 r_symmetry_vdw_other 0.192 r_nbtor_refined 0.185 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.106 r_xyhbond_nbd_other 0.089 r_nbtor_other 0.087 r_symmetry_hbond_refined 0.073 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 4971 Nucleic Acid Atoms Solvent Atoms 470 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing