2BHP

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


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 5 MM NAD.
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.179α = 90
b = 102.179β = 90
c = 278.614γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2002-11-26MSINGLE 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
11.85098.40.1114.13.799097-36.7
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)
11.81.8399.90.543.43.7

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 1UZB1.844.7694390478193.80.1480.1480.176RANDOM12.8
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]
1.121.071.12-2.25
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.9
c_scangle_it3.54
c_scbond_it2.47
c_mcangle_it1.64
c_angle_deg1.4
c_mcbond_it1.32
c_improper_angle_d0.94
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.9
c_scangle_it3.54
c_scbond_it2.47
c_mcangle_it1.64
c_angle_deg1.4
c_mcbond_it1.32
c_improper_angle_d0.94
c_bond_d0.006
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 Atoms8070
Nucleic Acid Atoms
Solvent Atoms1200
Heterogen Atoms190

Software

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