2EIT

Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-alanine and NAD


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J40PDB ENTRY 2j40

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.229330% MPD, 50MM SODIUM CITRATE/HCL, 5mM NAD+, 50mM L-alanine, 50MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4249.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.586α = 90
b = 101.586β = 90
c = 278.785γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2006-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.0SPring-8BL26B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.653099.50.0650.05822.43.7128737128737-314.5
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)
11.651.6998.40.230.1892.53.48480

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2j401.6527.96118360118360628396.380.161270.161270.160050.18395RANDOM13.978
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
r_dihedral_angle_2_deg34.7
r_dihedral_angle_4_deg16.096
r_dihedral_angle_3_deg12.646
r_dihedral_angle_1_deg6.135
r_scangle_it3.107
r_scbond_it1.867
r_angle_refined_deg1.268
r_mcangle_it1.015
r_mcbond_it0.552
r_metal_ion_refined0.335
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.7
r_dihedral_angle_4_deg16.096
r_dihedral_angle_3_deg12.646
r_dihedral_angle_1_deg6.135
r_scangle_it3.107
r_scbond_it1.867
r_angle_refined_deg1.268
r_mcangle_it1.015
r_mcbond_it0.552
r_metal_ion_refined0.335
r_nbtor_refined0.312
r_nbd_refined0.199
r_symmetry_vdw_refined0.177
r_symmetry_hbond_refined0.131
r_xyhbond_nbd_refined0.121
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8076
Nucleic Acid Atoms
Solvent Atoms905
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing