2CKP

Crystal structure of Human Choline Kinase alpha-2 in complex with ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NW1PDB ENTRY 1NW1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.50.01 M MGCL2, 15% PEG 3350, 0.2M NAF, pH 7.50
Crystal Properties
Matthews coefficientSolvent content
4.0369.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.271α = 90
b = 127.137β = 90
c = 158.742γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-IDAPS22-ID

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
13.11599.30.1520.389.619759
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)
13.13.2593.90.612.36.7

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 1NW13.11517590199099.30.2630.2560.329RANDOM51.31
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]
-2.690.282.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_3_deg20.44
r_dihedral_angle_4_deg18.221
r_dihedral_angle_1_deg6.678
r_scangle_it1.481
r_angle_refined_deg1.369
r_scbond_it0.885
r_mcangle_it0.687
r_mcbond_it0.379
r_symmetry_hbond_refined0.361
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.002
r_dihedral_angle_3_deg20.44
r_dihedral_angle_4_deg18.221
r_dihedral_angle_1_deg6.678
r_scangle_it1.481
r_angle_refined_deg1.369
r_scbond_it0.885
r_mcangle_it0.687
r_mcbond_it0.379
r_symmetry_hbond_refined0.361
r_symmetry_vdw_refined0.33
r_nbtor_refined0.312
r_nbd_refined0.232
r_xyhbond_nbd_refined0.159
r_chiral_restr0.097
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
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 Atoms4626
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing