☰ Navigation Tabs
Crystal structure of the SucA domain of Mycobacterium smegmatis KGD, post-decarboxylation intermediate from pyruvate (2-hydroxyethyl-ThDP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YIC PDB ENTRY 2YIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 59% MPD, 22.5 MM NA ACETATE PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.65 53.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.464 α = 99.68 b = 83.702 β = 98.87 c = 160.333 γ = 100.63
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 KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS 2012-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 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 2.3 41.86 97.6 0.08 8 2.4 172580 46.53
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 2.3 2.42 97.3 0.49 1.9 2.3
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 PDB ENTRY 2YIC 2.3 41.06 172547 8626 97.63 0.205 0.2034 0.2354 0.2352 RANDOM 50.37
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] -7.4557 0.8742 -2.2454 2.7212 0.174 4.7344
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.2 t_other_torsion 2.66 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.2 t_other_torsion 2.66 t_angle_deg 1.01 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 25040 Nucleic Acid Atoms Solvent Atoms 969 Heterogen Atoms 124
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing