3MWU

Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with bumped kinase inhibitor RM-1-95


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IGO3IGO, PROTEIN ONLY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1729827% PEG 3350, 0.27 M ammonium tartrate (pH 7.0), 6% PEG 400, 5 mM TCEP, 4 mM MgCl2, 2 mM CaCl2, 2 mM inhibitor, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.02α = 90
b = 55.97β = 104.79
c = 82.21γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2010-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
11.9858.0399.80.04611.15483.7136138534.8
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)
11.982.199.80.432.33.67

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3IGO, PROTEIN ONLY1.9842.0436121180899.80.1960.1940.229RANDOM55.41
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]
-0.370.78-0.140.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.227
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg14.233
r_dihedral_angle_1_deg5.58
r_scangle_it5.549
r_scbond_it3.704
r_mcangle_it3.257
r_mcbond_it2.011
r_angle_refined_deg1.218
r_angle_other_deg0.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.227
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg14.233
r_dihedral_angle_1_deg5.58
r_scangle_it5.549
r_scbond_it3.704
r_mcangle_it3.257
r_mcbond_it2.011
r_angle_refined_deg1.218
r_angle_other_deg0.856
r_mcbond_other0.601
r_chiral_restr0.071
r_bond_refined_d0.011
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 Atoms3607
Nucleic Acid Atoms
Solvent Atoms125
Heterogen Atoms32

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing