3RPZ

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


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
2.9758.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.92α = 90
b = 91.92β = 90
c = 169.63γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rMIRRORS2009-10-16MSINGLE 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
11.51501000.0860.08625.9137.657168-317.3

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 1KYH1.515057159289599.960.1350.1340.148RANDOM21.147
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]
-0.38-0.380.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.294
r_dihedral_angle_4_deg16.15
r_dihedral_angle_3_deg11.897
r_dihedral_angle_1_deg6.295
r_scangle_it4.713
r_angle_other_deg4.24
r_scbond_it2.948
r_angle_refined_deg2.155
r_mcangle_it1.89
r_mcbond_it1.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.294
r_dihedral_angle_4_deg16.15
r_dihedral_angle_3_deg11.897
r_dihedral_angle_1_deg6.295
r_scangle_it4.713
r_angle_other_deg4.24
r_scbond_it2.948
r_angle_refined_deg2.155
r_mcangle_it1.89
r_mcbond_it1.043
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_other0.011
r_gen_planes_refined0.01
r_bond_other_d
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2107
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms73

Software

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