2GB5

Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP2779.975% PEG MME 5000, 0.05M Acetic Acid, 0.052M Citrate_Na3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3647.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.287α = 90
b = 103.553β = 90
c = 57.27γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152003-10-18MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.9802, 1.0000ALS8.2.2

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
12.349.62999.10.0760.0765.73.426695
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)
12.32.3691.60.3840.38422.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.349.6126666134598.980.2010.1980.252RANDOM37.389
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]
-3.032.140.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.11
r_dihedral_angle_4_deg17.118
r_dihedral_angle_3_deg14.455
r_dihedral_angle_1_deg6.225
r_scangle_it5.296
r_scbond_it3.819
r_mcangle_it2.081
r_mcbond_it1.599
r_angle_refined_deg1.225
r_angle_other_deg0.768
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.11
r_dihedral_angle_4_deg17.118
r_dihedral_angle_3_deg14.455
r_dihedral_angle_1_deg6.225
r_scangle_it5.296
r_scbond_it3.819
r_mcangle_it2.081
r_mcbond_it1.599
r_angle_refined_deg1.225
r_angle_other_deg0.768
r_mcbond_other0.377
r_nbd_other0.175
r_nbtor_refined0.171
r_nbd_refined0.17
r_xyhbond_nbd_refined0.165
r_symmetry_vdw_other0.154
r_symmetry_hbond_refined0.152
r_symmetry_vdw_refined0.111
r_nbtor_other0.082
r_chiral_restr0.069
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4171
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling
SOLVEphasing