1VR6

Crystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase) (TM0343) from Thermotoga Maritima at 1.92 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RZMPDB entry 1RZM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP5.529335.0% Ethylene-Glycol, 0.1M Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.243.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.151α = 90
b = 74.226β = 90
c = 249.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315fixed-height exit beam, toroidal focusing mirror2004-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.2ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.9247.7698.790.06523.073.5710246444.73
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.9690.380.6591.492.634594

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 1RZM1.9247.7697241511198.540.17320.170890.21519RANDOM42.205
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]
0.01-0.290.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.389
r_dihedral_angle_4_deg20.19
r_dihedral_angle_3_deg14.676
r_scangle_it7.058
r_dihedral_angle_1_deg5.943
r_scbond_it5.247
r_mcangle_it3.095
r_mcbond_it2.113
r_angle_refined_deg1.516
r_angle_other_deg0.842
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.389
r_dihedral_angle_4_deg20.19
r_dihedral_angle_3_deg14.676
r_scangle_it7.058
r_dihedral_angle_1_deg5.943
r_scbond_it5.247
r_mcangle_it3.095
r_mcbond_it2.113
r_angle_refined_deg1.516
r_angle_other_deg0.842
r_mcbond_other0.604
r_symmetry_vdw_other0.298
r_symmetry_vdw_refined0.271
r_nbd_refined0.213
r_nbd_other0.192
r_xyhbond_nbd_refined0.18
r_symmetry_hbond_refined0.179
r_nbtor_refined0.172
r_chiral_restr0.093
r_nbtor_other0.086
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10375
Nucleic Acid Atoms
Solvent Atoms615
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement