1LR4

Room Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HCLBACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293PEG4000, sodium acetate, Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 142.55α = 90
b = 61.44β = 103.06
c = 45.41γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277IMAGE PLATEMARRESEARCHMirrors1996-10-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.1MPG/DESY, HAMBURGBW6

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1226.2940.1062.8258962434215.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.1184.90.1111.7

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 REPLACEMENTTHROUGHOUTBACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL)22623092124793.680.194870.192540.23675RANDOM27.212
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]
-2.27-1.322.2-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.714
r_dihedral_angle_1_deg4.069
r_scangle_it3.805
r_scbond_it2.34
r_mcangle_it1.649
r_angle_refined_deg1.52
r_angle_other_deg1.287
r_mcbond_it0.926
r_symmetry_hbond_refined0.465
r_nbd_refined0.248
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.714
r_dihedral_angle_1_deg4.069
r_scangle_it3.805
r_scbond_it2.34
r_mcangle_it1.649
r_angle_refined_deg1.52
r_angle_other_deg1.287
r_mcbond_it0.926
r_symmetry_hbond_refined0.465
r_nbd_refined0.248
r_symmetry_vdw_other0.226
r_nbd_other0.224
r_xyhbond_nbd_refined0.215
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_other0.145
r_symmetry_hbond_other0.142
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_other0.013
r_gen_planes_refined0.008
r_bond_other_d
r_nbtor_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2769
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms9

Software

Software
Software NamePurpose
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
REFMACrefinement
CCP4data scaling
X-PLORphasing