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Crystal structure of a stable adenylate kinase variant AKlse5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 26.5% (w/v) polyethylene glycol 4000, 150mM magnesium acetate, 100mM sodium cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.089 α = 90 b = 75.36 β = 89.996 c = 81.982 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 ADSC QUANTUM 270 2013-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.9793 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 1.67 81.98 97.6 50674 49458
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 1.68 1.74 95.7
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 1ZIN 1.67 50 48379 46923 2516 96.99 0.17868 0.17628 0.187 0.22327 0.232 RANDOM 26.64
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] -1.35 -0.46 -1.03 2.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 15.852 r_dihedral_angle_3_deg 13.4 r_long_range_B_refined 7.495 r_long_range_B_other 7.398 r_dihedral_angle_1_deg 6.081 r_scangle_other 4.171 r_scbond_it 2.748 r_scbond_other 2.747 r_angle_refined_deg 2.199
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.936 r_dihedral_angle_4_deg 15.852 r_dihedral_angle_3_deg 13.4 r_long_range_B_refined 7.495 r_long_range_B_other 7.398 r_dihedral_angle_1_deg 6.081 r_scangle_other 4.171 r_scbond_it 2.748 r_scbond_other 2.747 r_angle_refined_deg 2.199 r_mcangle_it 2.136 r_mcangle_other 2.136 r_mcbond_it 1.463 r_mcbond_other 1.462 r_angle_other_deg 0.946 r_chiral_restr 0.121 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3393 Nucleic Acid Atoms Solvent Atoms 401 Heterogen Atoms 118
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling