3DOO

Crystal structure of shikimate dehydrogenase from Staphylococcus epidermidis complexed with shikimate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DONPDB ENTRY 3DON

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.1M Sodium Cacodylate pH 6.5, 23% PEG 8000, 0.2M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.189α = 90
b = 52.529β = 96.14
c = 56.777γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-03-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.228.2399.20.1225.23.5213476
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)
2.22.2899.60.381.93.451347

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 3DON2.2151346166899.380.1920.1880.264RANDOM28.345
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]
-1-0.221.53-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.752
r_dihedral_angle_4_deg21.144
r_dihedral_angle_3_deg18.819
r_dihedral_angle_1_deg6.828
r_scangle_it4.603
r_scbond_it3.076
r_angle_refined_deg2.082
r_mcangle_it1.937
r_mcbond_it1.206
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.752
r_dihedral_angle_4_deg21.144
r_dihedral_angle_3_deg18.819
r_dihedral_angle_1_deg6.828
r_scangle_it4.603
r_scbond_it3.076
r_angle_refined_deg2.082
r_mcangle_it1.937
r_mcbond_it1.206
r_nbtor_refined0.314
r_symmetry_vdw_refined0.256
r_nbd_refined0.239
r_xyhbond_nbd_refined0.21
r_symmetry_hbond_refined0.171
r_chiral_restr0.138
r_bond_refined_d0.025
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2036
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms12

Software

Software
Software NamePurpose
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CNSphasing