3HP1

Crystal structure of human dCK R104M/D133A in complex with L-dT and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5ZPDB entry 1P5Z

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52951 microliter of protein-nucleoside-nucleotide mix and 1 microliter reservoir solution containing 0.9-1.5 M Trisodium citrate dihydrate and 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2846.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.78α = 90
b = 79.78β = 90
c = 93.7γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-08-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0000APS22-BM

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
12.33099.30.08914.4213710-3
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)
2.32.4598.20.2986.93

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 1P5Z2.313011826131095.160.210410.20490.26108RANDOM45.265
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]
1.311.31-2.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.044
r_dihedral_angle_3_deg18.256
r_dihedral_angle_4_deg15.173
r_dihedral_angle_1_deg5.261
r_scangle_it3.055
r_scbond_it1.983
r_mcangle_it1.475
r_angle_refined_deg1.402
r_mcbond_it0.85
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.044
r_dihedral_angle_3_deg18.256
r_dihedral_angle_4_deg15.173
r_dihedral_angle_1_deg5.261
r_scangle_it3.055
r_scbond_it1.983
r_mcangle_it1.475
r_angle_refined_deg1.402
r_mcbond_it0.85
r_nbtor_refined0.312
r_symmetry_vdw_refined0.218
r_xyhbond_nbd_refined0.217
r_nbd_refined0.216
r_symmetry_hbond_refined0.164
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1838
Nucleic Acid Atoms
Solvent Atoms91
Heterogen Atoms44

Software

Software
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction