☰ Navigation Tabs
Crystal structure of Escherichia coli ketopantoate reductase in a ternary complex with NADP+ and pantoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KS9 PDB entries 1KS9 and 1YJQ experimental model PDB 1YJQ PDB entries 1KS9 and 1YJQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 50mM HEPES-HCl, 35% v/v dioxane, 2 mM NADP+, 10 mM pantoate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.09 60.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.692 α = 90 b = 101.692 β = 90 c = 171.168 γ = 90
Symmetry Space Group P 41 21 2
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 315 2006-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.977 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 99.9 0.073 0.073 12.8 9.3 40670 40629 38.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.35 100 0.425 0.425 9.3 40629
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 entries 1KS9 and 1YJQ 2.3 43.94 38533 2032 99.92 0.1592 0.15621 0.215 0.2113 RANDOM 36.301
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.219 r_dihedral_angle_4_deg 18.431 r_dihedral_angle_3_deg 16.253 r_dihedral_angle_1_deg 5.975 r_scangle_it 5.385 r_mcangle_it 4.149 r_scbond_it 3.972 r_mcbond_it 3.04 r_angle_refined_deg 1.448 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.219 r_dihedral_angle_4_deg 18.431 r_dihedral_angle_3_deg 16.253 r_dihedral_angle_1_deg 5.975 r_scangle_it 5.385 r_mcangle_it 4.149 r_scbond_it 3.972 r_mcbond_it 3.04 r_angle_refined_deg 1.448 r_nbtor_refined 0.301 r_symmetry_hbond_refined 0.241 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4703 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing