3TQC

Structure of the pantothenate kinase (coaA) from Coxiella burnetii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ESMPDB CODE 1ESM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP9.52980.2 M sodium chloride, 10% PEG8000, 0.1 M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9157.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.214α = 90
b = 94.698β = 106.4
c = 75.398γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2011-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4C0.979NSLSX4C

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
12.310093.90.06222.245188846728-3
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)
12.32.34910.3064.53.82552

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 CODE 1ESM2.372.333797035570180293.680.213810.21090.26861RANDOM30.956
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]
0.15-0.34-1.91.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.683
r_dihedral_angle_4_deg16.399
r_dihedral_angle_3_deg14.877
r_dihedral_angle_1_deg5.591
r_scangle_it2.51
r_scbond_it1.541
r_angle_refined_deg1.247
r_mcangle_it0.882
r_angle_other_deg0.831
r_mcbond_it0.453
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.683
r_dihedral_angle_4_deg16.399
r_dihedral_angle_3_deg14.877
r_dihedral_angle_1_deg5.591
r_scangle_it2.51
r_scbond_it1.541
r_angle_refined_deg1.247
r_mcangle_it0.882
r_angle_other_deg0.831
r_mcbond_it0.453
r_mcbond_other0.103
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4994
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms54

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling