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Crystal structure of a stable adenylate kinase variant AKlse4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MKG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 32% (w/v) polyethylene glycol 4000, 250mM MgCl2, 100mM Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.817 α = 90 b = 71.02 β = 95.13 c = 45.555 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 270 2013-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9795 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.37 50 97 45588 44220
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 1.37 1.42 95.1
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 (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 4MKG 1.37 49.32 43373 41955 2265 96.73 0.18128 0.17915 0.1888 0.22029 0.2265 RANDOM 26.268
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] 0.44 -1.28 -0.46 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.683 r_dihedral_angle_4_deg 17.163 r_dihedral_angle_3_deg 12.297 r_long_range_B_refined 8.48 r_long_range_B_other 8.372 r_dihedral_angle_1_deg 5.54 r_scangle_other 4.615 r_scbond_it 3.07 r_scbond_other 3.068 r_angle_refined_deg 2.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.683 r_dihedral_angle_4_deg 17.163 r_dihedral_angle_3_deg 12.297 r_long_range_B_refined 8.48 r_long_range_B_other 8.372 r_dihedral_angle_1_deg 5.54 r_scangle_other 4.615 r_scbond_it 3.07 r_scbond_other 3.068 r_angle_refined_deg 2.51 r_mcangle_other 1.882 r_mcangle_it 1.88 r_mcbond_it 1.499 r_mcbond_other 1.496 r_angle_other_deg 1.357 r_chiral_restr 0.151 r_bond_refined_d 0.026 r_gen_planes_refined 0.015 r_gen_planes_other 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1706 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 59
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling