2EII

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J40 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.229330% MPD, 50MM SODIUM CITRATE/HCL, 5mM NAD+, 50mM L-valine, 100MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4549.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.208α = 90
b = 102.208β = 90
c = 278.432γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU JUPITER 210mirrors2006-06-07MSINGLE 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
11.8892.8599.40.0370.0333.93.58794087940-316
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)
11.881.9599.40.1080.0877.53.18818

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 SYNTHESISTHROUGHOUT2j401.88508352683526441099.420.135560.135560.133850.16812RANDOM15.511
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]
0.760.380.76-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.089
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg12.66
r_dihedral_angle_1_deg6.255
r_scangle_it3.386
r_scbond_it1.981
r_angle_refined_deg1.295
r_mcangle_it1.068
r_mcbond_it0.561
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.089
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg12.66
r_dihedral_angle_1_deg6.255
r_scangle_it3.386
r_scbond_it1.981
r_angle_refined_deg1.295
r_mcangle_it1.068
r_mcbond_it0.561
r_nbtor_refined0.311
r_nbd_refined0.195
r_symmetry_vdw_refined0.175
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.127
r_chiral_restr0.089
r_metal_ion_refined0.074
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8076
Nucleic Acid Atoms
Solvent Atoms976
Heterogen Atoms234

Software

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