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The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManDMJ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other PREVIOUSLY SOLVED NATIVE APO STRUCTURE
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 2.15 42.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.248 α = 90 b = 85.285 β = 90 c = 100.613 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 2013-05-22 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 1.3 43.3 99.8 0.06 16.6 8 173270 -3.7 12.6
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 1.3 1.32 99.6 0.92 2.2 8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PREVIOUSLY SOLVED NATIVE APO STRUCTURE 1.3 65.06 164705 8466 99.69 0.17697 0.1753 0.20949 0.2166 RANDOM
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] 0.5 -0.37 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 24.927 r_sphericity_free 23.542 r_dihedral_angle_3_deg 11.807 r_sphericity_bonded 8.588 r_dihedral_angle_1_deg 5.399 r_long_range_B_refined 3.106 r_rigid_bond_restr 2.948 r_long_range_B_other 2.861 r_scangle_other 2.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 24.927 r_sphericity_free 23.542 r_dihedral_angle_3_deg 11.807 r_sphericity_bonded 8.588 r_dihedral_angle_1_deg 5.399 r_long_range_B_refined 3.106 r_rigid_bond_restr 2.948 r_long_range_B_other 2.861 r_scangle_other 2.696 r_scbond_it 2.45 r_scbond_other 2.45 r_mcangle_it 2.022 r_mcangle_other 2.022 r_mcbond_it 1.813 r_mcbond_other 1.803 r_angle_refined_deg 1.326 r_angle_other_deg 0.817 r_chiral_restr 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5353 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing