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Ruminococcus gnavus sialic acid aldolase catalytic lysine mutant in complex with sialic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris/Bicine pH 8.5, 20% ethylene glycol, 10% PEG 8000, soaked with 5mM Neu5Ac prior to plunge freezing
Crystal Properties Matthews coefficient Solvent content 2.82 56.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.05 α = 90 b = 121.74 β = 119.49 c = 74.47 γ = 90
Symmetry Space Group C 1 2 1
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-F 2018-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.892 68.431 54.3 0.117 0.128 0.051 0.997 7.7 6.2 31874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.892 2.145 8.7 1.006 1.095 0.429 0.656 1.8 6.2
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 6RAB 1.892 68.43 30310 1566 53.5 0.19 0.188 0.1981 0.23 0.2431 RANDOM 37.47
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] 0.2454 0.2884 2.5624 -2.8079
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.99 t_omega_torsion 3.2 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.99 t_omega_torsion 3.2 t_angle_deg 1.09 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4662 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing