2GNI

PKA fivefold mutant model of Rho-kinase with inhibitor Fasudil (HA1077)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otheran unpublished structure of the binary complex of PKA C alpha wildtype enzyme with PKI(5-24)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5278Methanol, LiCl, MesBisTris, EDTA, DTT, Mega8, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
2.5652.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.227α = 90
b = 75.959β = 90
c = 80.396γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARRESEARCH2004-07-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2730.881002102421024
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.272.39100

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTan unpublished structure of the binary complex of PKA C alpha wildtype enzyme with PKI(5-24)2.2730.88199581995810651000.192220.188340.26817RANDOM28.473
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]
1.070.15-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.241
r_scangle_it3.567
r_scbond_it2.204
r_angle_refined_deg1.596
r_mcangle_it1.47
r_angle_other_deg0.88
r_mcbond_it0.79
r_symmetry_vdw_refined0.415
r_symmetry_vdw_other0.301
r_symmetry_hbond_refined0.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.241
r_scangle_it3.567
r_scbond_it2.204
r_angle_refined_deg1.596
r_mcangle_it1.47
r_angle_other_deg0.88
r_mcbond_it0.79
r_symmetry_vdw_refined0.415
r_symmetry_vdw_other0.301
r_symmetry_hbond_refined0.283
r_nbd_other0.24
r_nbd_refined0.204
r_xyhbond_nbd_refined0.144
r_chiral_restr0.098
r_nbtor_other0.088
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_gen_planes_other0.004
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2978
Nucleic Acid Atoms
Solvent Atoms217
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing