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X-ray structure of PKAc with ADP, free phosphate ion, CP20, magnesium 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 2.34 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.304 α = 90 b = 79.228 β = 90 c = 97.82 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++ 2013-03-29 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 1.9 40 98.6 0.042 30.15 3.8 32017
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) 1.9 1.97 91.9 0.389 2.5 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4DH3 1.9 20 32017 1595 89.9 0.186 0.186 0.2646 0.2314 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 6 3302.2
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.147 s_non_zero_chiral_vol 0.096 s_zero_chiral_vol 0.095 s_similar_adp_cmpnt 0.08 s_angle_d 0.032 s_from_restr_planes 0.0305 s_bond_d 0.015 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2957 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 65
Software Software Software Name Purpose PHASER phasing SHELX refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing SHELXL-97 refinement