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The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with MSMSMe
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 2.21 44.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.55 α = 90 b = 85.226 β = 90 c = 102.003 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 2014-04-24 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 43.8 100 0.06 21.5 12.8 178799 -3.7 15.6
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 99.9 1.22 2.3 10.4
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 PREVIOUSLY SOLVED NATIVE APO STRUCTURE 1.3 65.4 170002 8695 99.99 0.12247 0.12097 0.1321 0.15161 0.159 RANDOM 22.501
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] 0.03 -0.09 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.601 r_sphericity_free 36.348 r_dihedral_angle_4_deg 25.646 r_sphericity_bonded 12.137 r_dihedral_angle_3_deg 11.548 r_dihedral_angle_1_deg 5.679 r_scangle_it 3.142 r_scbond_it 2.761 r_rigid_bond_restr 2.535 r_mcangle_it 2.462
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.601 r_sphericity_free 36.348 r_dihedral_angle_4_deg 25.646 r_sphericity_bonded 12.137 r_dihedral_angle_3_deg 11.548 r_dihedral_angle_1_deg 5.679 r_scangle_it 3.142 r_scbond_it 2.761 r_rigid_bond_restr 2.535 r_mcangle_it 2.462 r_mcbond_it 2.048 r_mcbond_other 2.048 r_angle_refined_deg 1.386 r_angle_other_deg 0.86 r_symmetry_vdw_refined 0.358 r_symmetry_vdw_other 0.321 r_nbd_refined 0.269 r_symmetry_hbond_refined 0.237 r_nbtor_refined 0.19 r_nbd_other 0.184 r_xyhbond_nbd_refined 0.125 r_xyhbond_nbd_other 0.118 r_chiral_restr 0.088 r_nbtor_other 0.081 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_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 5382 Nucleic Acid Atoms Solvent Atoms 1035 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing