2HEO

General Structure-Based Approach to the Design of Protein Ligands: Application to the Design of Kv1.2 Potassium Channel Blockers.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629325% PEG 4000, 0.2M Na/K phosphate, 0.1M MES, 5mM Bmercapto-ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6453.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.91α = 90
b = 79.91β = 90
c = 55.335γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray2005-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

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
11.76599.90.0820.08216.17222261125.8
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)
11.71.791000.4170.4173.173227

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 1J751.7202224121057112999.820.24140.2480.2410.30507RANDOM34.061
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]
0.510.250.51-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.543
r_dihedral_angle_4_deg21.039
r_dihedral_angle_3_deg18.332
r_dihedral_angle_1_deg5.198
r_scangle_it2.695
r_angle_refined_deg2.007
r_scbond_it2.002
r_mcangle_it1.314
r_mcbond_it0.85
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.543
r_dihedral_angle_4_deg21.039
r_dihedral_angle_3_deg18.332
r_dihedral_angle_1_deg5.198
r_scangle_it2.695
r_angle_refined_deg2.007
r_scbond_it2.002
r_mcangle_it1.314
r_mcbond_it0.85
r_nbtor_refined0.303
r_nbd_refined0.277
r_symmetry_hbond_refined0.268
r_xyhbond_nbd_refined0.219
r_symmetry_vdw_refined0.208
r_chiral_restr0.158
r_bond_refined_d0.013
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms924
Nucleic Acid Atoms246
Solvent Atoms228
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing