2YXG

Crystal structure of Dihyrodipicolinate Synthase (dapA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O5K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1Oil-batch6.529318% PEG 8000, 0.1M Cacodylate, 0.2M Ca Acetate, pH 6.5, Oil-batch, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.3748.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.469α = 90
b = 76.532β = 106.87
c = 101.863γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.10.979SRSPX10.1

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
12.25097.60.0673.95998558517-3
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)
2.22.2882.60.2112.74918

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 REPLACEMENTTHROUGHOUT1O5K2.22055463296597.470.161150.157740.22444RANDOM26.881
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]
-1.97-0.90.980.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.514
r_dihedral_angle_4_deg19.352
r_dihedral_angle_3_deg16.061
r_dihedral_angle_1_deg6.852
r_scangle_it5.369
r_scbond_it3.374
r_angle_refined_deg1.825
r_mcangle_it1.721
r_mcbond_it1.164
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.514
r_dihedral_angle_4_deg19.352
r_dihedral_angle_3_deg16.061
r_dihedral_angle_1_deg6.852
r_scangle_it5.369
r_scbond_it3.374
r_angle_refined_deg1.825
r_mcangle_it1.721
r_mcbond_it1.164
r_nbtor_refined0.311
r_nbd_refined0.246
r_symmetry_vdw_refined0.229
r_xyhbond_nbd_refined0.16
r_chiral_restr0.129
r_symmetry_hbond_refined0.128
r_bond_refined_d0.022
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8849
Nucleic Acid Atoms
Solvent Atoms700
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing