4NQ1

Legionella pneumophila dihydrodipicolinate synthase with first substrate pyruvate bound in the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QZEPDB ENTRY 3QZE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1102810.1M Tris, 0.2M magnesium chloride, 10%(W/V) PEG 8000, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal Properties
Matthews coefficientSolvent content
2.6453.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.31α = 90
b = 89.31β = 90
c = 290.18γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rSILICON MIRRORS (ADAPTIVE AND U- BENT)2012-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX2Australian SynchrotronMX2

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
11.6536.2798.90.1089.14.68190811.76
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)
11.651.7499.80.3434.25

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3QZE1.6536.278325380488102097.90.1480.1470.187RANDOM18.9
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]
0.510.260.51-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.483
r_dihedral_angle_4_deg16.781
r_dihedral_angle_3_deg13.606
r_dihedral_angle_1_deg6.104
r_scangle_it5.807
r_scbond_it3.602
r_angle_refined_deg2.189
r_mcangle_it1.77
r_mcbond_it1.148
r_chiral_restr0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.483
r_dihedral_angle_4_deg16.781
r_dihedral_angle_3_deg13.606
r_dihedral_angle_1_deg6.104
r_scangle_it5.807
r_scbond_it3.602
r_angle_refined_deg2.189
r_mcangle_it1.77
r_mcbond_it1.148
r_chiral_restr0.18
r_bond_refined_d0.027
r_gen_planes_refined0.012
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
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 Atoms4420
Nucleic Acid Atoms
Solvent Atoms918
Heterogen Atoms27

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling