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Crystal structure of a stable adenylate kinase variant AKlse6
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 2.46 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.814 α = 90 b = 76.512 β = 90.2 c = 85.13 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 2013-07-21 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 50 100 54822 54822
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 1.67 1.73 100
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 52088 52020 2780 99.87 0.17036 0.16834 0.1811 0.20817 0.2172 RANDOM 28.438
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] -0.68 -0.36 -0.78 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.484 r_dihedral_angle_4_deg 13.015 r_dihedral_angle_3_deg 12.964 r_long_range_B_refined 9.129 r_long_range_B_other 9.128 r_dihedral_angle_1_deg 5.787 r_scangle_other 4.857 r_scbond_it 3.292 r_scbond_other 3.291 r_angle_other_deg 2.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.484 r_dihedral_angle_4_deg 13.015 r_dihedral_angle_3_deg 12.964 r_long_range_B_refined 9.129 r_long_range_B_other 9.128 r_dihedral_angle_1_deg 5.787 r_scangle_other 4.857 r_scbond_it 3.292 r_scbond_other 3.291 r_angle_other_deg 2.688 r_mcangle_other 2.43 r_angle_refined_deg 2.428 r_mcangle_it 2.428 r_mcbond_it 1.745 r_mcbond_other 1.745 r_chiral_restr 0.133 r_bond_refined_d 0.025 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3383 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 118
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling