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The structure of GH113 beta-mannanase AaManA from Alicyclobacillus acidocaldarius in complex with ManMIm
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 2.06 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.82 α = 90 b = 75.89 β = 90 c = 91.48 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 2012-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.47 58.41 99.7 0.06 14 6.3 52176 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 1.47 1.51 99 0.71 2.6 6.2
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 1.47 58.41 49455 2659 99.67 0.17274 0.17043 0.181 0.21511 0.2257 RANDOM 21.867
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] 3.04 -3.58 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.384 r_rigid_bond_restr 27.306 r_sphericity_free 23.15 r_sphericity_bonded 15.67 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 6.41 r_scangle_it 4.262 r_scbond_it 3.962 r_mcangle_it 3.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.384 r_rigid_bond_restr 27.306 r_sphericity_free 23.15 r_sphericity_bonded 15.67 r_dihedral_angle_4_deg 13.583 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 6.41 r_scangle_it 4.262 r_scbond_it 3.962 r_mcangle_it 3.423 r_mcbond_it 2.972 r_mcbond_other 2.958 r_angle_refined_deg 1.508 r_angle_other_deg 0.834 r_symmetry_vdw_refined 0.297 r_symmetry_vdw_other 0.264 r_nbd_refined 0.24 r_symmetry_hbond_refined 0.2 r_nbtor_refined 0.192 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.09 r_nbtor_other 0.083 r_xyhbond_nbd_other 0.06 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 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 2453 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing