1LPU

Low 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 1A6OPDB entry 1a6o

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.1293PEG3350, Tris/HCl, sodium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.19α = 90
b = 59.758β = 103.41
c = 45.082γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCEdouble mirrors1998-08-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5711.5418

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
11.8669.6990.08428.48.8315543123018
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)
1.861.9289.80.47347.52845

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1a6o1.8669.0129657157299.560.206370.204210.2476RANDOM22.307
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]
-1.77-1.451.25-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.592
r_dihedral_angle_1_deg4.019
r_scangle_it3.408
r_scbond_it2.14
r_mcangle_it1.512
r_angle_refined_deg1.438
r_angle_other_deg1.264
r_mcbond_it0.86
r_symmetry_vdw_other0.277
r_nbd_refined0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg15.592
r_dihedral_angle_1_deg4.019
r_scangle_it3.408
r_scbond_it2.14
r_mcangle_it1.512
r_angle_refined_deg1.438
r_angle_other_deg1.264
r_mcbond_it0.86
r_symmetry_vdw_other0.277
r_nbd_refined0.24
r_symmetry_hbond_refined0.222
r_nbd_other0.219
r_xyhbond_nbd_refined0.206
r_symmetry_vdw_refined0.152
r_xyhbond_nbd_other0.124
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_other0.01
r_gen_planes_refined0.007
r_symmetry_hbond_other0.002
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 Atoms2744
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms9

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement