7A06

Structure of human CKa1 in complex with compound o


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3G15 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 3350 magensium nitrate
Crystal Properties
Matthews coefficientSolvent content
2.3246.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.374α = 90
b = 61.374β = 90
c = 221.07γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2013-05-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.987DiamondI04-1

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
11.820099.90.112.68.540416
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)
11.81.90.653

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 REPLACEMENTTHROUGHOUT3G151.861.3739176114699.890.189830.188670.22994RANDOM23.462
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]
0.150.15-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.435
r_dihedral_angle_4_deg16.09
r_dihedral_angle_3_deg14.688
r_long_range_B_refined5.983
r_long_range_B_other5.983
r_dihedral_angle_1_deg5.37
r_scangle_other2.936
r_mcangle_it2.031
r_mcangle_other2.031
r_scbond_it1.791
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.435
r_dihedral_angle_4_deg16.09
r_dihedral_angle_3_deg14.688
r_long_range_B_refined5.983
r_long_range_B_other5.983
r_dihedral_angle_1_deg5.37
r_scangle_other2.936
r_mcangle_it2.031
r_mcangle_other2.031
r_scbond_it1.791
r_scbond_other1.791
r_angle_refined_deg1.385
r_mcbond_it1.231
r_mcbond_other1.229
r_angle_other_deg0.884
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2941
Nucleic Acid Atoms
Solvent Atoms357
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing