4NMA

Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA in complex with L-tetrahydro-2-furoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NMCPDB ENTRY 4NMC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.529825-28% PEG550 MME, 0.05-0.15 M Bis-Tris, pH 6.3-6.5, 0.05 M calcium chloride, MICROBATCH, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8556.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.619α = 90
b = 151.743β = 90
c = 176.205γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152012-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.10147.52998.50.11113.314694714694725.39
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)
12.1012.2196.70.6050.6051.13.220880

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 4NMC2.10146.1411.33146604734098.070.17490.17280.2135FROM OPEN FORM STRUCTURE23.5921
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.2
f_angle_d1.05
f_chiral_restr0.071
f_bond_d0.007
f_plane_restr0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15129
Nucleic Acid Atoms
Solvent Atoms738
Heterogen Atoms202

Software

Software
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing