3DJC

CRYSTAL STRUCTURE OF PANTOTHENATE KINASE FROM LEGIONELLA PNEUMOPHILA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5100MM MES PH 6.5, 28% PEG MME 5K, 250MM AMMONIUM PHOSPHATE, VAPOR DIFFUSION, TEMPERATURE 294K, pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.4850.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.394α = 90
b = 134.571β = 93.24
c = 134.404γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMAR CCD 165 mm2007-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.355097.50.1250.12531.914065162.35
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4394.90.8330.8330.41.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.420124742390897.50.2610.2590.313RANDOM63.24
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]
-0.05-0.480.17-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.654
r_dihedral_angle_3_deg19.33
r_dihedral_angle_4_deg16.158
r_scangle_it13.94
r_scbond_it11.242
r_mcangle_it8.698
r_mcbond_it6.433
r_dihedral_angle_1_deg5.843
r_angle_refined_deg1.245
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.654
r_dihedral_angle_3_deg19.33
r_dihedral_angle_4_deg16.158
r_scangle_it13.94
r_scbond_it11.242
r_mcangle_it8.698
r_mcbond_it6.433
r_dihedral_angle_1_deg5.843
r_angle_refined_deg1.245
r_nbtor_refined0.297
r_symmetry_hbond_refined0.215
r_xyhbond_nbd_refined0.169
r_nbd_refined0.13
r_symmetry_vdw_refined0.092
r_chiral_restr0.085
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms23182
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms66

Software

Software
Software NamePurpose
SHELXDphasing
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling