1YON

Escherichia coli ketopantoate reductase in complex with 2-monophosphoadenosine-5'-diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KS9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529010% 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 coefficientSolvent content
3.0759.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.318α = 90
b = 65.833β = 90
c = 98.207γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.939ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.955099.20.11523.213.6292302898528.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.95292.70.4762.61760

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1KS91.9519.722898527466147198.610.168150.168150.166020.20986RANDOM31.052
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
KeyRefinement Restraint Deviation
r_scangle_it6.856
r_dihedral_angle_1_deg5.979
r_mcangle_it4.607
r_scbond_it4.562
r_mcbond_it3.169
r_angle_refined_deg1.753
r_angle_other_deg0.847
r_symmetry_vdw_refined0.33
r_symmetry_vdw_other0.302
r_nbd_other0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it6.856
r_dihedral_angle_1_deg5.979
r_mcangle_it4.607
r_scbond_it4.562
r_mcbond_it3.169
r_angle_refined_deg1.753
r_angle_other_deg0.847
r_symmetry_vdw_refined0.33
r_symmetry_vdw_other0.302
r_nbd_other0.25
r_nbd_refined0.212
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.136
r_chiral_restr0.098
r_nbtor_other0.09
r_bond_refined_d0.02
r_gen_planes_other0.015
r_gen_planes_refined0.011
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2280
Nucleic Acid Atoms
Solvent Atoms212
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing