2FZM

Structure of the E. coli PutA proline dehydrogenase domain reduced by dithionite and complexed with SO2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TJ0PDB Entry: 1TJ0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.7293Crystals were grown in 13-15% PEG 3350, 60-190 mM citrate buffer. Prior to data collection a crystal was soaked in excess Na dithionite in order to reduce the FAD cofactor., pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8256.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.11α = 90
b = 141.424β = 90
c = 145.7γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray173CCDADSC QUANTUM 42003-11-15MSINGLE 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)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
12.35098.20.0719.733078
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3894.20.465

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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: 1TJ02.346.133307116351000.2120.2120.2090.257RANDOM36.941
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]
-0.64.69-4.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.447
r_scangle_it3.444
r_scbond_it2.126
r_angle_refined_deg1.446
r_mcangle_it1.364
r_angle_other_deg0.829
r_mcbond_it0.726
r_nbd_other0.229
r_symmetry_vdw_other0.22
r_nbd_refined0.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.447
r_scangle_it3.444
r_scbond_it2.126
r_angle_refined_deg1.446
r_mcangle_it1.364
r_angle_other_deg0.829
r_mcbond_it0.726
r_nbd_other0.229
r_symmetry_vdw_other0.22
r_nbd_refined0.209
r_symmetry_vdw_refined0.173
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.14
r_nbtor_other0.086
r_chiral_restr0.076
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3460
Nucleic Acid Atoms
Solvent Atoms117
Heterogen Atoms56

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction