2BRB

Structure-based Design of Novel Chk1 Inhibitors: Insights into Hydrogen Bonding and Protein-Ligand Affinity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IA8PDB ENTRY 1IA8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.50
Crystal Properties
Matthews coefficientSolvent content
2.956.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.993α = 90
b = 65.77β = 94.29
c = 58.36γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.13096.60.08134200502
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)
12.12.1883.20.442.72

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1IA82.157.7418612100497.90.2430.2410.272RANDOM38.67
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]
-1.5-0.120.041.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.92
r_scangle_it1.304
r_angle_refined_deg0.99
r_mcangle_it0.837
r_scbond_it0.691
r_mcbond_it0.461
r_nbd_refined0.159
r_symmetry_vdw_refined0.114
r_xyhbond_nbd_refined0.07
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg3.92
r_scangle_it1.304
r_angle_refined_deg0.99
r_mcangle_it0.837
r_scbond_it0.691
r_mcbond_it0.461
r_nbd_refined0.159
r_symmetry_vdw_refined0.114
r_xyhbond_nbd_refined0.07
r_chiral_restr0.066
r_symmetry_hbond_refined0.063
r_bond_refined_d0.006
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2184
Nucleic Acid Atoms
Solvent Atoms228
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing