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Ruminococcus bromii Amy12-D392A with 63-a-D-glucosyl-maltotriosyl-maltotriose
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 63-a-D-glucosyl-maltotriosyl-maltotriose 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 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.981 α = 90 b = 99.107 β = 90 c = 167.236 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 2016-10-05 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 2.05 85.3 99.8 0.99 5.9 7.3 49996
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 2.05 2.12 0.64
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 2.05 85.26 47508 2487 99.79 0.1824 0.1799 0.1865 0.2318 0.2361 RANDOM 23.062
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] -0.04 -1.12 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.396 r_sphericity_free 25.858 r_dihedral_angle_4_deg 14.364 r_dihedral_angle_3_deg 12.992 r_sphericity_bonded 8.971 r_dihedral_angle_1_deg 6.814 r_angle_refined_deg 0.877 r_angle_other_deg 0.753 r_rigid_bond_restr 0.32 r_chiral_restr 0.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.396 r_sphericity_free 25.858 r_dihedral_angle_4_deg 14.364 r_dihedral_angle_3_deg 12.992 r_sphericity_bonded 8.971 r_dihedral_angle_1_deg 6.814 r_angle_refined_deg 0.877 r_angle_other_deg 0.753 r_rigid_bond_restr 0.32 r_chiral_restr 0.039 r_bond_refined_d 0.004 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5878 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement xia2 data scaling PHASER phasing PDB_EXTRACT data extraction xia2 data reduction