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Catalytic and ubiqutin-associated domains of MARK2/PAR-1: K82R mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y8G PDB ENTRY 1Y8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG3350, Ammonium Sulphate, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.191 α = 90 b = 121.191 β = 90 c = 99.66 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2004-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8043 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.105 51.78 98.2 0.109 14 14813 14813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.105 3.15 99.3 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1Y8G 3.105 51.78 14814 14814 740 98.2 0.20235 0.20235 0.19983 0.1986 0.25108 0.2505 RANDOM 68.393
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] 0.35 0.17 0.35 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_3_deg 21.516 r_dihedral_angle_4_deg 19.398 r_dihedral_angle_1_deg 7.57 r_angle_refined_deg 1.955 r_symmetry_hbond_refined 0.395 r_nbtor_refined 0.342 r_nbd_refined 0.269 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.21 r_dihedral_angle_3_deg 21.516 r_dihedral_angle_4_deg 19.398 r_dihedral_angle_1_deg 7.57 r_angle_refined_deg 1.955 r_symmetry_hbond_refined 0.395 r_nbtor_refined 0.342 r_nbd_refined 0.269 r_symmetry_vdw_refined 0.222 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.114 r_bond_refined_d 0.022 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4667 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement