4RVL

CHK1 kinase domain with diazacarbazole compound 7: 3-(2-hydroxyphenyl)-9H-pyrrolo[2,3-b:5,4-c']dipyridine-6-carbonitrile


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZYS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4292HEPES, isopropanol, PEG 8000, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.4950.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.902α = 90
b = 65.73β = 94.03
c = 57.787γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDRIGAKU SATURN 944+2008-11-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.845099.40.04926.33.62868428518-324

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUT1ZYS1.8520-32868427091142799.380.190.184140.182420.21559RANDOM30.096
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]
-0.850.180.91-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.106
r_dihedral_angle_3_deg12.458
r_dihedral_angle_4_deg12.147
r_dihedral_angle_1_deg5.371
r_scangle_it3.808
r_mcangle_it3.45
r_mcbond_it3.012
r_scbond_it2.814
r_angle_refined_deg1.316
r_angle_other_deg0.859
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.106
r_dihedral_angle_3_deg12.458
r_dihedral_angle_4_deg12.147
r_dihedral_angle_1_deg5.371
r_scangle_it3.808
r_mcangle_it3.45
r_mcbond_it3.012
r_scbond_it2.814
r_angle_refined_deg1.316
r_angle_other_deg0.859
r_mcbond_other0.521
r_symmetry_vdw_other0.281
r_symmetry_vdw_refined0.204
r_nbd_refined0.198
r_nbd_other0.184
r_nbtor_refined0.174
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.13
r_nbtor_other0.082
r_chiral_restr0.069
r_bond_refined_d0.01
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 Atoms2101
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms22

Software

Software
Software NamePurpose
JDirectordata collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling