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Escherichia coli ketopantoate reductase in complex with 2-monophosphoadenosine-5'-diphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KS9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 290 10% 2-methyl-2,4-pentanediol, 0.1M sodium acetate, 2mM NADPH, 2mM pantoate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.318 α = 90 b = 65.833 β = 90 c = 98.207 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 2004-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.939 ESRF ID14-4
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 1.95 50 99.2 0.115 23.2 13.6 29230 28985 28.2
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 1.95 2 92.7 0.476 2.6 1760
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1KS9 1.95 19.7 2 28985 27466 1471 98.61 0.16815 0.16815 0.16602 0.1776 0.20986 0.2196 RANDOM 31.052
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] 1.56 -0.75 -0.81
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.856 r_dihedral_angle_1_deg 5.979 r_mcangle_it 4.607 r_scbond_it 4.562 r_mcbond_it 3.169 r_angle_refined_deg 1.753 r_angle_other_deg 0.847 r_symmetry_vdw_refined 0.33 r_symmetry_vdw_other 0.302 r_nbd_other 0.25
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 6.856 r_dihedral_angle_1_deg 5.979 r_mcangle_it 4.607 r_scbond_it 4.562 r_mcbond_it 3.169 r_angle_refined_deg 1.753 r_angle_other_deg 0.847 r_symmetry_vdw_refined 0.33 r_symmetry_vdw_other 0.302 r_nbd_other 0.25 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.098 r_nbtor_other 0.09 r_bond_refined_d 0.02 r_gen_planes_other 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2280 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing