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Structure of the catalytic domain (BcGH76) of the Bacillus circulans GH76 alpha mannanase, Aman6.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K7X PDB ENTRY 3K7X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.23 44.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.843 α = 90 b = 85.419 β = 90 c = 102.024 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 2M 2014-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.4 43.8 98.4 0.07 16.7 8.3 141868 -3.7 14
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 1.4 1.42 96.3 1.37 1.7 8.1
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 3K7X 1.4 65.49 134900 6900 98.12 0.11786 0.116 0.1315 0.15423 0.1643 RANDOM 20.257
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] 0.43 -0.49 0.07
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.671 r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 22.991 r_sphericity_bonded 12.079 r_dihedral_angle_3_deg 11.325 r_dihedral_angle_1_deg 5.247 r_scangle_it 2.951 r_scbond_it 2.541 r_mcangle_it 2.092 r_rigid_bond_restr 1.855
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 40.671 r_dihedral_angle_2_deg 37.21 r_dihedral_angle_4_deg 22.991 r_sphericity_bonded 12.079 r_dihedral_angle_3_deg 11.325 r_dihedral_angle_1_deg 5.247 r_scangle_it 2.951 r_scbond_it 2.541 r_mcangle_it 2.092 r_rigid_bond_restr 1.855 r_mcbond_it 1.693 r_mcbond_other 1.643 r_angle_refined_deg 1.256 r_angle_other_deg 0.84 r_symmetry_vdw_refined 0.286 r_symmetry_vdw_other 0.274 r_nbd_refined 0.256 r_nbtor_refined 0.185 r_nbd_other 0.177 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.08 r_nbtor_other 0.076 r_symmetry_hbond_refined 0.034 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_xyhbond_nbd_other 0.004 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 5408 Nucleic Acid Atoms Solvent Atoms 965 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing