3RPH

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis co-crystallized with ATP/Mg2+.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1KYHPDB ENTRY 1KYH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.005 M ATP, 0.18 M Magnesium Cloride, 13.5%(v/v) PEG 400, 10%(v/v) Glycerol, 0.09 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9658.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.869α = 90
b = 91.869β = 90
c = 169.403γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2010-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97918APS19-BM

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.75501000.0860.08625.9137.636858-321.9
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)RedundancyNumber Unique Reflections (All)
11.751.7899.90.9130.9132.0826.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1KYH1.755036858184299.850.1540.1530.182RANDOM29.761
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]
-0.87-0.871.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.092
r_dihedral_angle_4_deg17.912
r_dihedral_angle_3_deg11.656
r_dihedral_angle_1_deg6.202
r_scangle_it4.989
r_angle_other_deg4.205
r_scbond_it3.013
r_mcangle_it2.014
r_angle_refined_deg1.74
r_mcbond_it1.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.092
r_dihedral_angle_4_deg17.912
r_dihedral_angle_3_deg11.656
r_dihedral_angle_1_deg6.202
r_scangle_it4.989
r_angle_other_deg4.205
r_scbond_it3.013
r_mcangle_it2.014
r_angle_refined_deg1.74
r_mcbond_it1.138
r_chiral_restr0.105
r_bond_refined_d0.019
r_gen_planes_other0.014
r_gen_planes_refined0.009
r_mcbond_other0.003
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2107
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing