1TIW

Crystal structure of E. coli PutA proline dehydrogenase domain (residues 86-669) complexed with L-Tetrahydro-2-furoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1K87PDB entry 1K87

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.729513-15% PEG 3000 or PEG 3350, 60-190 mM citrate, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.958

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.588α = 90
b = 141.358β = 90
c = 145.897γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173CCDCUSTOM-MADE2003-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97856APS19-ID

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
1299980.0680.068247.95104949933
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)
122.07910.3520.3524.26.74169

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 REPLACEMENTTHROUGHOUTPDB entry 1K87224.84499324744024921000.2160.215650.213780.25262RANDOM24.822
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]
-0.354.08-3.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.566
r_scangle_it3.316
r_scbond_it2.077
r_angle_refined_deg1.396
r_mcangle_it1.287
r_angle_other_deg0.83
r_mcbond_it0.72
r_symmetry_vdw_other0.244
r_nbd_other0.237
r_nbd_refined0.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.566
r_scangle_it3.316
r_scbond_it2.077
r_angle_refined_deg1.396
r_mcangle_it1.287
r_angle_other_deg0.83
r_mcbond_it0.72
r_symmetry_vdw_other0.244
r_nbd_other0.237
r_nbd_refined0.206
r_xyhbond_nbd_refined0.16
r_symmetry_vdw_refined0.138
r_symmetry_hbond_refined0.097
r_nbtor_other0.083
r_chiral_restr0.081
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_gen_planes_other0.005
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3545
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing