2IY6

1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND CITRATE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UZBPDB ENTRY 1UZB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.240% MPD, 50MM SODIUM CITRATE PH 5.2.
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.047α = 90
b = 102.047β = 90
c = 278.901γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC CCDMIRRORS2006-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B2SPring-8BL44B2

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
11.83099.70.0442.53.8100192-3
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)
11.81.861000.09143.9

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 1UZB1.83095147495999.70.140.1390.17RANDOM11.05
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_deg35.067
r_dihedral_angle_4_deg15.258
r_dihedral_angle_3_deg12.061
r_dihedral_angle_1_deg6.052
r_scangle_it3.287
r_scbond_it1.92
r_angle_refined_deg1.212
r_mcangle_it1.004
r_mcbond_it0.528
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.067
r_dihedral_angle_4_deg15.258
r_dihedral_angle_3_deg12.061
r_dihedral_angle_1_deg6.052
r_scangle_it3.287
r_scbond_it1.92
r_angle_refined_deg1.212
r_mcangle_it1.004
r_mcbond_it0.528
r_nbtor_refined0.31
r_nbd_refined0.193
r_symmetry_vdw_refined0.172
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.119
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms8076
Nucleic Acid Atoms
Solvent Atoms1157
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling