2J40

1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound inhibitor L-proline and NAD.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BJKPDB ENTRY 2BJK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.2PROTEIN WAS CRYSTALLIZED FROM 37.5% MRD, 50 MM SODIUM CITRATE, PH 5.2; THEN SOAKED IN 2MM NAD, 100MM L-PROLINE, 50 MM SODIUM ACETATE PH5.2.
Crystal Properties
Matthews coefficientSolvent content
2.450

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.043α = 90
b = 102.043β = 90
c = 278.6γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDMIRRORS2006-05-24MSINGLE 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
12.13099.70.111.13.262989-3
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)
12.12.1898.90.3222.7

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 2BJK2.13059782319399.70.1420.140.189RANDOM19.21
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]
1.320.661.32-1.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg18.366
r_dihedral_angle_3_deg13.903
r_dihedral_angle_1_deg9.954
r_scangle_it3.939
r_scbond_it2.455
r_angle_refined_deg1.536
r_mcangle_it1.275
r_mcbond_it0.707
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.976
r_dihedral_angle_4_deg18.366
r_dihedral_angle_3_deg13.903
r_dihedral_angle_1_deg9.954
r_scangle_it3.939
r_scbond_it2.455
r_angle_refined_deg1.536
r_mcangle_it1.275
r_mcbond_it0.707
r_nbtor_refined0.308
r_nbd_refined0.199
r_symmetry_vdw_refined0.189
r_xyhbond_nbd_refined0.137
r_symmetry_hbond_refined0.128
r_chiral_restr0.103
r_bond_refined_d0.017
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8078
Nucleic Acid Atoms
Solvent Atoms788
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
REFMACphasing