1YJQ

Crystal structure of ketopantoate reductase in complex with NADP+


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP529010% MPD, 0.1M Sodium Acetate, 2mM NADP+, 2mM ketopantoate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.1260.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.833α = 90
b = 66.138β = 90
c = 98.808γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.979SRSPX14.2

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
12.0955.0599.70.0921426.224200223.4
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)
2.12.1599.90.4363.21560

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1KS92.09282420022838123198.870.161730.161730.159950.19368RANDOM22.598
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]
-0.140.72-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.201
r_scangle_it5.49
r_scbond_it3.484
r_mcangle_it2.458
r_angle_refined_deg1.903
r_mcbond_it1.387
r_angle_other_deg0.929
r_nbd_other0.278
r_symmetry_vdw_other0.276
r_symmetry_vdw_refined0.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.201
r_scangle_it5.49
r_scbond_it3.484
r_mcangle_it2.458
r_angle_refined_deg1.903
r_mcbond_it1.387
r_angle_other_deg0.929
r_nbd_other0.278
r_symmetry_vdw_other0.276
r_symmetry_vdw_refined0.223
r_nbd_refined0.217
r_xyhbond_nbd_refined0.212
r_symmetry_hbond_refined0.164
r_chiral_restr0.114
r_nbtor_other0.089
r_bond_refined_d0.024
r_gen_planes_other0.013
r_gen_planes_refined0.01
r_bond_other_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2302
Nucleic Acid Atoms
Solvent Atoms230
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing