4DRS

Crystal structure of Cryptosporidium parvum 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 DROP42770.4-0.8 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0459.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.895α = 90
b = 136.941β = 90
c = 77.233γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2004-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.99987APS19-BM

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
12.550970.0616.14.247349
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)
12.52.898.50.285.74.2

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 1PKL2.549.713750445005234497.780.215230.21340.24949RANDOM62.028
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]
0.09-0.320.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.718
r_dihedral_angle_4_deg16.954
r_dihedral_angle_3_deg12.634
r_dihedral_angle_1_deg4.128
r_scangle_it1.816
r_mcangle_it1.205
r_scbond_it1.021
r_angle_refined_deg0.915
r_mcbond_it0.651
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.718
r_dihedral_angle_4_deg16.954
r_dihedral_angle_3_deg12.634
r_dihedral_angle_1_deg4.128
r_scangle_it1.816
r_mcangle_it1.205
r_scbond_it1.021
r_angle_refined_deg0.915
r_mcbond_it0.651
r_chiral_restr0.06
r_mcbond_other0.055
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
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 Atoms7288
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing