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Ruminococcus bromii Amy12-D392A with maltoheptaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 8.75 - 8.9 mg/ml of protein and 10 mM maltoheptaose via hanging drop against a well solution containing 16% PEG 3350, 4% glycerol, 0.3 ammonium acetate, and 0.1 M Bis-Tris pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.029 α = 90 b = 98.231 β = 90 c = 170.279 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 120 CCD MARMOSAIC 300 mm CCD 2016-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.979 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.42 85.23 96 0.99 7.5 4.9 29648
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.51 0.7
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 7LSA 2.42 85.14 28148 1500 95.95 0.1875 0.1854 0.193 0.2284 0.2331 RANDOM 27.159
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] -1.32 1.3 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.595 r_sphericity_free 26.545 r_sphericity_bonded 17.273 r_dihedral_angle_4_deg 14.306 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 6.129 r_angle_refined_deg 0.762 r_angle_other_deg 0.711 r_rigid_bond_restr 0.404 r_chiral_restr 0.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.595 r_sphericity_free 26.545 r_sphericity_bonded 17.273 r_dihedral_angle_4_deg 14.306 r_dihedral_angle_3_deg 12.139 r_dihedral_angle_1_deg 6.129 r_angle_refined_deg 0.762 r_angle_other_deg 0.711 r_rigid_bond_restr 0.404 r_chiral_restr 0.031 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5874 Nucleic Acid Atoms Solvent Atoms 285 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction