2BRG

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 = 45.136α = 90
b = 65.79β = 102.02
c = 54.683γ = 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
12.13099.10.096.73.2183862
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)
12.12.18990.4311

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 1IA82.1301689190796.80.2120.2070.294RANDOM46.02
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]
-2.12-1.52-0.331.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.238
r_scangle_it3.427
r_scbond_it2.24
r_angle_refined_deg1.801
r_mcangle_it1.593
r_angle_other_deg0.965
r_mcbond_it0.908
r_symmetry_hbond_refined0.35
r_symmetry_vdw_other0.255
r_symmetry_vdw_refined0.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.238
r_scangle_it3.427
r_scbond_it2.24
r_angle_refined_deg1.801
r_mcangle_it1.593
r_angle_other_deg0.965
r_mcbond_it0.908
r_symmetry_hbond_refined0.35
r_symmetry_vdw_other0.255
r_symmetry_vdw_refined0.232
r_nbd_other0.228
r_nbd_refined0.222
r_xyhbond_nbd_refined0.214
r_chiral_restr0.107
r_nbtor_other0.09
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_gen_planes_other0.006
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms2089
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing