2BJA

Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NADH


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 36% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD,CA.5MM DELTA1-PYRROLINE-5 CARBOXYLATE AND 50 MM SODIUM ACETATE/HCL, PH 5.2.
Crystal Properties
Matthews coefficientSolvent content
2.550.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.007α = 90
b = 102.007β = 90
c = 278.319γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2004-02-14MSINGLE 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
11.9401000.0817.26485247-313.4
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)
11.91.941000.462.153

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 1UZB1.937.2982153417896.50.1760.1760.212RANDOM25.4
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]
6.153.966.15-12.3
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.7
c_scangle_it2.9
c_scbond_it2
c_mcangle_it1.54
c_angle_deg1.4
c_mcbond_it1.11
c_improper_angle_d0.89
c_bond_d0.007
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.7
c_scangle_it2.9
c_scbond_it2
c_mcangle_it1.54
c_angle_deg1.4
c_mcbond_it1.11
c_improper_angle_d0.89
c_bond_d0.007
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 Atoms8075
Nucleic Acid Atoms
Solvent Atoms808
Heterogen Atoms80

Software

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