3NCG

Activated Calcium-Dependent Protein Kinase 1 from Cryptosporidium parvum (CpCDPK1) in complex with bumped kinase inhibitor NM-PP1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MWU3mwu, 3igo
experimental modelPDB 3IGO3mwu, 3igo

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP729832% PEG 3350, 0.35 M di-ammonium tartrate (not pH'ed), 5 mM TCEP, 3 mM MgCl2, 1 mM CaCl2, 2 mM inhibitor, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.991α = 90
b = 55.968β = 104.78
c = 81.972γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442009-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

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
12.493595.30.0928.13.717762552.9
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)
12.492.5997.20.6492.13.71775

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 SYNTHESISTHROUGHOUT3mwu, 3igo2.4933.581772490794.820.2530.250.305RANDOM58.73
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]
-1.750.64-0.572.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.133
r_dihedral_angle_4_deg18.018
r_dihedral_angle_3_deg15.638
r_dihedral_angle_1_deg5.672
r_scangle_it4.361
r_scbond_it2.906
r_mcangle_it2.634
r_mcbond_it1.555
r_angle_refined_deg1.105
r_angle_other_deg0.803
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.133
r_dihedral_angle_4_deg18.018
r_dihedral_angle_3_deg15.638
r_dihedral_angle_1_deg5.672
r_scangle_it4.361
r_scbond_it2.906
r_mcangle_it2.634
r_mcbond_it1.555
r_angle_refined_deg1.105
r_angle_other_deg0.803
r_mcbond_other0.342
r_chiral_restr0.058
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3418
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms27

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing