2V8Z

Crystal Structure of YagE, a prophage protein belonging to the dihydrodipicolinic acid synthase family from E. coli K12


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V9DPDB ENTRY 2V9D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5100 MM HEPES PH 6.5, 200 MM MGCL2, 25% PEG 3350, RT
Crystal Properties
Matthews coefficientSolvent content
2.0941.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.689α = 90
b = 156.494β = 90
c = 55.884γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS-IVMIRRORS2006-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
12.095099.40.146.16.773987-3
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)
12.092.1696.30.595.9

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 2V9D2.219.9260553325299.80.1920.190.232RANDOM5.45
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]
0.08-0.07-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.857
r_dihedral_angle_4_deg19.034
r_dihedral_angle_3_deg17.3
r_dihedral_angle_1_deg12.53
r_scangle_it3.03
r_scbond_it2.017
r_angle_refined_deg1.788
r_mcangle_it0.969
r_mcbond_it0.702
r_symmetry_vdw_refined0.363
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.857
r_dihedral_angle_4_deg19.034
r_dihedral_angle_3_deg17.3
r_dihedral_angle_1_deg12.53
r_scangle_it3.03
r_scbond_it2.017
r_angle_refined_deg1.788
r_mcangle_it0.969
r_mcbond_it0.702
r_symmetry_vdw_refined0.363
r_nbtor_refined0.305
r_nbd_refined0.205
r_xyhbond_nbd_refined0.158
r_chiral_restr0.155
r_symmetry_hbond_refined0.108
r_bond_refined_d0.017
r_gen_planes_refined0.006
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 Atoms9014
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing