☰ Navigation Tabs
Structure of LpxC bound to the reaction product UDP-(3-O-(R-3-hydroxymyristoyl))-glucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P3G PDB ENTRY 3P3G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 293 0.4 M sodium phosphate monobasic, 0.8 M potassium phosphate dibasic, 0.2 M CAPS, pH 10.5, 50 mM lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.25 62.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.973 α = 90 b = 103.52 β = 103.96 c = 103.968 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 CCD ADSC QUANTUM 210 2010-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.0 APS 17-ID
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 2.59 100 96 0.044 17.2 3.6 51839 66.57
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 2.59 2.73 79.3 0.424 2.3 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3P3G 2.59 50.45 51830 2646 95.66 0.1989 0.1966 0.2052 0.2402 0.2524 RANDOM 64.8643
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] 3.8769 2.4831 -10.1569 6.28
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.24 t_omega_torsion 2.15 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.24 t_omega_torsion 2.15 t_angle_deg 1.28 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9361 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 232
Software Software Software Name Purpose BUSTER-TNT refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction XDS data scaling PHASER phasing BUSTER refinement