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Crystal structure of adenylate kinase variant AKlse3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DKV PDB entry 3DKV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 29% PEG MME 2000, 100mM NaCl, 100mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.003 α = 90 b = 76.688 β = 95.3 c = 77.993 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 MARMOSAIC 300 mm CCD 2007-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 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 1.53 50 98.9 59416
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 1.53 1.58
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 3DKV 1.58 38.84 54455 2758 99.76 0.202 0.2 0.1991 0.239 0.2397 RANDOM 18.394
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] -0.03 -0.06 -0.32 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.705 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 5.318 r_scangle_it 3.201 r_scbond_it 2.064 r_angle_refined_deg 1.508 r_mcangle_it 1.293 r_mcbond_it 0.833 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.705 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 13.704 r_dihedral_angle_1_deg 5.318 r_scangle_it 3.201 r_scbond_it 2.064 r_angle_refined_deg 1.508 r_mcangle_it 1.293 r_mcbond_it 0.833 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.224 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.083 r_metal_ion_refined 0.019 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3356 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing