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Crystal structure of adenylate kinase variant AKlse1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKY PDB entry 1AKY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 25% PEG 4000, 400mM NaCl, 100 mM Na Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.49 50.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.624 α = 90 b = 62.056 β = 90 c = 86.995 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 CCD MARMOSAIC 300 mm CCD 2007-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97297 APS 23-ID-D
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 1.69 50.51 95 26423
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 1.69 1.75
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 1AKY 1.82 25.47 22301 1145 99.86 0.177 0.174 0.1737 0.231 0.2282 RANDOM 16.918
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] 0.4 -0.69 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.689 r_dihedral_angle_4_deg 13.723 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 5.332 r_scangle_it 2.852 r_scbond_it 1.917 r_angle_refined_deg 1.582 r_mcangle_it 1.067 r_mcbond_it 0.775 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.689 r_dihedral_angle_4_deg 13.723 r_dihedral_angle_3_deg 12.994 r_dihedral_angle_1_deg 5.332 r_scangle_it 2.852 r_scbond_it 1.917 r_angle_refined_deg 1.582 r_mcangle_it 1.067 r_mcbond_it 0.775 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.209 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1687 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 71
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling