2BJK

Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NAD and citrate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UZBPDB ENTRY 1UZB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.2PROTEIN WAS CRYSTALLIZED FROM 32% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD AND 10MM MGCL2.
Crystal Properties
Matthews coefficientSolvent content
2.550.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.436α = 90
b = 102.436β = 90
c = 278.559γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS-VMIRRORS2002-10-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B1SPring-8BL26B1

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
11.045097.60.0716.92.5511404-0.512
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)
11.041.05940.591.72.1

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 1UZB1.433.29211739624498.60.1560.1560.17RANDOM13.9
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]
1.140.741.14-2.27
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.8
c_scangle_it2.52
c_scbond_it1.74
c_angle_deg1.4
c_mcangle_it1.15
c_improper_angle_d0.98
c_mcbond_it0.81
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.8
c_scangle_it2.52
c_scbond_it1.74
c_angle_deg1.4
c_mcangle_it1.15
c_improper_angle_d0.98
c_mcbond_it0.81
c_bond_d0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8076
Nucleic Acid Atoms
Solvent Atoms1361
Heterogen Atoms188

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing