3B1F | pdb_00003b1f

Crystal structure of prephenate dehydrogenase from Streptococcus mutans


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.4464.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.34α = 90
b = 145.624β = 90
c = 77.552γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 210MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C1PAL/PLS6C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.152.724626

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.136.5324626131497.470.195310.193240.23640.234010.2643RANDOM22.404
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]
-0.14-0.170.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.886
r_dihedral_angle_4_deg22.722
r_dihedral_angle_3_deg16.237
r_sphericity_free12.054
r_dihedral_angle_1_deg6.631
r_scangle_it5.914
r_sphericity_bonded5.158
r_scbond_it4.209
r_rigid_bond_restr2.652
r_mcangle_it2.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.886
r_dihedral_angle_4_deg22.722
r_dihedral_angle_3_deg16.237
r_sphericity_free12.054
r_dihedral_angle_1_deg6.631
r_scangle_it5.914
r_sphericity_bonded5.158
r_scbond_it4.209
r_rigid_bond_restr2.652
r_mcangle_it2.456
r_angle_refined_deg2.012
r_mcbond_it1.534
r_chiral_restr0.127
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2238
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms44

Software

Software
Software NamePurpose
HKL-2000data collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling