☰ Navigation Tabs
Crystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate phosphonoethyl ester (PESP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YIC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 60% MPD, 22.5 mM Na acetate
Crystal Properties Matthews coefficient Solvent content 2.69 54.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.39 α = 99.54 b = 83.96 β = 98.78 c = 160.68 γ = 100.89
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 2012-03-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97895 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.09 78.48 97.4 0.07 0.048 0.997 10 2.9 233909 35.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.12 96.4 0.565 0.399 0.83 2.2 2.8
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 FOURIER SYNTHESIS THROUGHOUT 2YIC 2.09 21.07 233039 11680 97.4 0.233 0.232 0.234 0.246 0.2511 RANDOM 43.36
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] -10.374 -3.3678 0.4197 3.3983 0.0538 6.9756
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3 t_other_torsion 2.63 t_angle_deg 0.94 t_bond_d 0.009 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 t_other_torsion 2.63 t_angle_deg 0.94 t_bond_d 0.009 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 25237 Nucleic Acid Atoms Solvent Atoms 847 Heterogen Atoms 164
Software Software Software Name Purpose BUSTER refinement XDS data reduction autoPROC data scaling REFMAC phasing