2QKR

Cryptosporidium parvum cyclin-dependent kinase cgd5_2510 with indirubin 3'-monoxime bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OB3PDB entry 1OB3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52988% PEG 20000, 16% Glycerol, 0.1 M MES pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8657.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.133α = 90
b = 64.133β = 90
c = 201.153γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2007-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ DW1.5418

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
12.43599.60.0490.03218.26.61731117311
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)
2.42.491000.8370.4812.96.51669

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1OB32.633.67136281362869199.610.24940.24940.24690.2996RANDOM64.992
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]
0.120.12-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.529
r_dihedral_angle_4_deg21.778
r_dihedral_angle_3_deg18.412
r_dihedral_angle_1_deg5.36
r_scangle_it1.77
r_angle_refined_deg1.243
r_scbond_it1.058
r_mcangle_it0.911
r_mcbond_it0.487
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.529
r_dihedral_angle_4_deg21.778
r_dihedral_angle_3_deg18.412
r_dihedral_angle_1_deg5.36
r_scangle_it1.77
r_angle_refined_deg1.243
r_scbond_it1.058
r_mcangle_it0.911
r_mcbond_it0.487
r_nbtor_refined0.313
r_nbd_refined0.206
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.146
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2178
Nucleic Acid Atoms
Solvent Atoms23
Heterogen Atoms21

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing