4MXA

CDPK1 from Neospora caninum in complex with inhibitor RM-1-132


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4M97PDB ENTRY 4M97

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7298protein solution: 25 mM HEPES pH 7.0, 0.5 M NaCl, 5% glycerol, 5 mM DTT, 20 mM EGTA, 3mg/ml protein, 0.2 mM RM-1-132, 1% DMSO; crystallization buffer: 30% PEG 3350, 0.2 M ammonium citrate, 0.1 M BisTris pH 5.3, 5 mM DTT, vapor diffusion, sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0640.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.22α = 90
b = 72.53β = 99.28
c = 65.65γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.97939SSRLBL12-2

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
1347.5989.10.3763.62.88027
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)
133.2189.70.01812.71432

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 SYNTHESISTHROUGHOUTPDB ENTRY 4M97347.63709732878.520.25380.25260.2793RANDOM73.6112
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]
-2.980.40.971.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.389
r_dihedral_angle_3_deg16.412
r_dihedral_angle_4_deg15.291
r_dihedral_angle_1_deg5.533
r_mcangle_it2.602
r_mcbond_it1.509
r_mcbond_other1.507
r_angle_refined_deg1.43
r_angle_other_deg0.801
r_chiral_restr0.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.389
r_dihedral_angle_3_deg16.412
r_dihedral_angle_4_deg15.291
r_dihedral_angle_1_deg5.533
r_mcangle_it2.602
r_mcbond_it1.509
r_mcbond_other1.507
r_angle_refined_deg1.43
r_angle_other_deg0.801
r_chiral_restr0.076
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3670
Nucleic Acid Atoms
Solvent Atoms25
Heterogen Atoms30

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
MOSFLMdata reduction