3HQN

Apo crystal structure of Leishmania mexicana(LmPYK)pyruvate kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PKLPDB ENTRY 1PKL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.227710-16% PEG8000, 20mM triethanolamine-HCl, 50mM MgCl2, 100mM KCl, 10-15% glycerol, pH7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0659.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.579α = 90
b = 167.333β = 90
c = 132.199γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmmirrors2008-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.98ESRFBM14

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
1252.1399.80.09915.27.2899102230.2
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)
122.111000.58837.313071

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 1PKL239.3285394450499.70.170640.168630.20906RANDOM25.8
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]
0.05-0.410.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.592
r_dihedral_angle_4_deg22.089
r_dihedral_angle_3_deg15.957
r_scangle_it6.457
r_dihedral_angle_1_deg6.264
r_scbond_it4.036
r_mcangle_it2.225
r_angle_refined_deg2.052
r_mcbond_it1.313
r_chiral_restr0.181
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.592
r_dihedral_angle_4_deg22.089
r_dihedral_angle_3_deg15.957
r_scangle_it6.457
r_dihedral_angle_1_deg6.264
r_scbond_it4.036
r_mcangle_it2.225
r_angle_refined_deg2.052
r_mcbond_it1.313
r_chiral_restr0.181
r_bond_refined_d0.029
r_gen_planes_refined0.011
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7512
Nucleic Acid Atoms
Solvent Atoms734
Heterogen Atoms32

Software

Software
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
SCALAdata scaling