3RQ8

Crystal Structure of ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Bacillus subtilis soaked with P1,P5-Di(adenosine-5') pentaphosphate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.18 M Magnesium Cloride, 19%(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
2.9758.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.904α = 90
b = 91.904β = 90
c = 169.493γ = 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
11.9501000.1010.10128.22613.128945-323.8
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)
11.91.931000.8760.8762.511.9

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 1KYH1.95028895146799.840.1670.1660.19RANDOM27.829
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]
-1-12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.698
r_dihedral_angle_4_deg15.607
r_dihedral_angle_3_deg11.867
r_dihedral_angle_1_deg6.339
r_scangle_it4.371
r_scbond_it2.68
r_angle_refined_deg1.676
r_mcangle_it1.564
r_angle_other_deg0.946
r_mcbond_it0.899
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.698
r_dihedral_angle_4_deg15.607
r_dihedral_angle_3_deg11.867
r_dihedral_angle_1_deg6.339
r_scangle_it4.371
r_scbond_it2.68
r_angle_refined_deg1.676
r_mcangle_it1.564
r_angle_other_deg0.946
r_mcbond_it0.899
r_mcbond_other0.282
r_chiral_restr0.099
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2107
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms85

Software

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