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Enzyme-ligand complex of P. aeruginosa PMM/PGM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P5G PMM/PGM bound to glucose 6-phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties Matthews coefficient Solvent content 2.2 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.7 α = 90 b = 74.193 β = 90 c = 84.836 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 100 CCD ADSC QUANTUM 4 mirrors 2003-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
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 1.6 25 99.1 0.074 32.1 8.2 59165 58633 18.6
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 1.6 1.66 98.3 0.491 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION rigid body refinement followed by regular refinement THROUGHOUT PMM/PGM bound to glucose 6-phosphate 1.6 25 59514 56042 2945 99.15 0.1621 0.1568 0.15565 0.17901 0.1856 RANDOM 14.863
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] -0.52 -0.42 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.878 r_scangle_it 3.442 r_scbond_it 2.078 r_angle_refined_deg 1.387 r_mcangle_it 1.268 r_angle_other_deg 0.998 r_mcbond_it 0.692 r_symmetry_vdw_other 0.278 r_symmetry_vdw_refined 0.246 r_nbd_other 0.244
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.878 r_scangle_it 3.442 r_scbond_it 2.078 r_angle_refined_deg 1.387 r_mcangle_it 1.268 r_angle_other_deg 0.998 r_mcbond_it 0.692 r_symmetry_vdw_other 0.278 r_symmetry_vdw_refined 0.246 r_nbd_other 0.244 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.14 r_metal_ion_refined 0.09 r_chiral_restr 0.085 r_nbtor_other 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3436 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing