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X-ray structure of PKAc with ATP, CP20, calcium ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DH3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 100 mM MES pH 6.5, 5 mM DTT, 15-20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.37 54.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.755 α = 90 b = 79.331 β = 90 c = 98.176 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 IMAGE PLATE RIGAKU RAXIS IV++ 2013-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.95 40 98 0.047 27.25 3.9 30637
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) 1.95 2.02 91.8 0.349 2.4 3.1
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 FREE R-VALUE 4DH3 1.95 20 30637 1536 91.3 0.1852 0.185 0.1747 0.2519 0.2225 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 1 3284.5
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.075 s_non_zero_chiral_vol 0.034 s_zero_chiral_vol 0.03 s_from_restr_planes 0.0245 s_angle_d 0.02 s_anti_bump_dis_restr 0.011 s_bond_d 0.005 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2914 Nucleic Acid Atoms Solvent Atoms 333 Heterogen Atoms 64
Software Software Software Name Purpose PHASER phasing SHELX refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing SHELXL-97 refinement