3BE4

Crystal structure of Cryptosporidium parvum adenylate kinase cgd5_3360


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AK2PDB entry 1AK2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72932.5 M Ammonium sulfate, 0.1 M BTP pH 7.0, 10 mM Adenosine-5-pentaphosphate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9958.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.175α = 90
b = 101.175β = 90
c = 72.433γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-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
11.620990.0670.057113.6361673616719.543
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)
11.61.661000.4660.4383.353.73686

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 1AK21.619.373613036130181498.980.1640.1620.202RANDOM25.453
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.836
r_dihedral_angle_4_deg18.141
r_dihedral_angle_3_deg15.529
r_dihedral_angle_1_deg6.95
r_scangle_it5.429
r_scbond_it3.965
r_angle_refined_deg2.939
r_mcangle_it2.748
r_mcbond_it1.98
r_symmetry_hbond_refined0.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.836
r_dihedral_angle_4_deg18.141
r_dihedral_angle_3_deg15.529
r_dihedral_angle_1_deg6.95
r_scangle_it5.429
r_scbond_it3.965
r_angle_refined_deg2.939
r_mcangle_it2.748
r_mcbond_it1.98
r_symmetry_hbond_refined0.412
r_chiral_restr0.37
r_nbtor_refined0.319
r_symmetry_vdw_refined0.268
r_nbd_refined0.225
r_xyhbond_nbd_refined0.213
r_bond_refined_d0.035
r_gen_planes_refined0.017
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1655
Nucleic Acid Atoms
Solvent Atoms259
Heterogen Atoms70

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection