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Crystal Structure of Apoenzyme Alpha-kinase Domain of Myosin-II Heavy Chain Kinase A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LKM PDB entry 3LKM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 277.15 PEG8000, PEG300, glycerol, magnesium chloride, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.62 53.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.298 α = 90 b = 103.469 β = 89.99 c = 167.811 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 300 mm CCD 2010-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.0332 APS 23-ID-B
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 2.9 40 98.3 0.14 16.72 6.5 63388 61697 75
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 2.9 3 86.4 0.619 1.33 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3LKM 2.9 40 58572 3125 97.32 0.2423 0.2409 0.2415 0.268 0.2673 RANDOM 79.993
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] 3.52 0.05 0.99 -4.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.705 r_dihedral_angle_4_deg 20.237 r_dihedral_angle_3_deg 16.878 r_mcangle_it 6.552 r_dihedral_angle_1_deg 6.276 r_mcbond_it 4.037 r_mcbond_other 4.032 r_angle_refined_deg 1.564 r_angle_other_deg 1.493 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.705 r_dihedral_angle_4_deg 20.237 r_dihedral_angle_3_deg 16.878 r_mcangle_it 6.552 r_dihedral_angle_1_deg 6.276 r_mcbond_it 4.037 r_mcbond_other 4.032 r_angle_refined_deg 1.564 r_angle_other_deg 1.493 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15997 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building