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Structure of human Membrane-associated Tyrosine- and Threonine-specific cdc2-inhibitory kinase MYT1 (PKMYT1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C30 PDB ENTRIES 2C30 and 3CR0 experimental model PDB 3CR0 PDB ENTRIES 2C30 and 3CR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 20% PEG 3350, 0.2M KSCN, 0.1M Bis-Tris Propane, pH 6.5, 10% Ethylene glycol , VAPOR DIFFUSION, SITTING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.12 42.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.4 α = 90 b = 56.3 β = 90 c = 114.66 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M Kirkpatrick Baez bimorph mirror pair 2010-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9245 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 35.32 98.6 0.087 13.2 6.2 32606 32553 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.79 95.3 0.445 3.2 4 4497
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 ENTRIES 2C30 and 3CR0 1.7 30.08 2 32553 30914 1639 98.32 0.1522 0.1522 0.14995 0.1591 0.19495 0.2025 RANDOM 14.802
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] -0.32 0.79 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.81 r_dihedral_angle_4_deg 18.656 r_dihedral_angle_3_deg 11.539 r_scangle_it 8.994 r_scbond_it 6.631 r_dihedral_angle_1_deg 5.154 r_mcangle_it 4.161 r_mcbond_it 2.762 r_angle_refined_deg 1.56 r_angle_other_deg 0.985
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.81 r_dihedral_angle_4_deg 18.656 r_dihedral_angle_3_deg 11.539 r_scangle_it 8.994 r_scbond_it 6.631 r_dihedral_angle_1_deg 5.154 r_mcangle_it 4.161 r_mcbond_it 2.762 r_angle_refined_deg 1.56 r_angle_other_deg 0.985 r_mcbond_other 0.842 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2170 Nucleic Acid Atoms Solvent Atoms 350 Heterogen Atoms 48
Software Software Software Name Purpose GDA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling