2EJL

Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-serine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BHPPDB ENTRY 2bhp

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.229330% MPD, 50MM SODIUM CITRATE/HCL, THEN SOAKED IN 30% MPD, 50mM L-serine, 50MM SODIUM Acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4549.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.04α = 90
b = 102.04β = 90
c = 279.352γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210mirrors2006-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B21.0SPring-8BL44B2

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
11.5251000.0540.04832.95.6173614173614-313.1
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)
11.51.531000.4560.4073.85.411553

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 2bhp1.525156770156770827895.020.183560.183560.182440.20465RANDOM12.548
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]
0.370.190.37-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.134
r_dihedral_angle_4_deg14.552
r_dihedral_angle_3_deg12.459
r_dihedral_angle_1_deg10.759
r_scangle_it2.85
r_scbond_it1.721
r_angle_refined_deg1.216
r_mcangle_it0.958
r_mcbond_it0.539
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.134
r_dihedral_angle_4_deg14.552
r_dihedral_angle_3_deg12.459
r_dihedral_angle_1_deg10.759
r_scangle_it2.85
r_scbond_it1.721
r_angle_refined_deg1.216
r_mcangle_it0.958
r_mcbond_it0.539
r_nbtor_refined0.311
r_nbd_refined0.193
r_symmetry_vdw_refined0.176
r_metal_ion_refined0.127
r_xyhbond_nbd_refined0.117
r_symmetry_hbond_refined0.116
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8078
Nucleic Acid Atoms
Solvent Atoms985
Heterogen Atoms128

Software

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