1Y8G

Catalytic and ubiqutin-associated domains of MARK2/PAR-1: Inactive double mutant with selenomethionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherpartially refined model of a similar construct obtained by combination of MR and MIR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5293PEG 5000 MME, TACSIMATE, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8656.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.822α = 90
b = 118.822β = 90
c = 105.38γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8031EMBL/DESY, HAMBURGX13

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
12.50146.399.90.09917.97.26292592925958.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.5012.54100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONotherTHROUGHOUTpartially refined model of a similar construct obtained by combination of MR and MIR2.50146.32925929259151499.970.201360.201360.197760.26834RANDOM43.887
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]
0.350.180.35-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.035
r_dihedral_angle_3_deg19.696
r_dihedral_angle_4_deg19.37
r_dihedral_angle_1_deg6.249
r_scangle_it3.368
r_scbond_it2.249
r_angle_refined_deg1.527
r_mcangle_it1.468
r_mcbond_it0.936
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.035
r_dihedral_angle_3_deg19.696
r_dihedral_angle_4_deg19.37
r_dihedral_angle_1_deg6.249
r_scangle_it3.368
r_scbond_it2.249
r_angle_refined_deg1.527
r_mcangle_it1.468
r_mcbond_it0.936
r_nbtor_refined0.318
r_nbd_refined0.232
r_symmetry_hbond_refined0.187
r_symmetry_vdw_refined0.17
r_xyhbond_nbd_refined0.167
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.005
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4913
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
MLPHAREphasing
REFMACrefinement