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Crystal structure of an adenylate kinase mutant--AKm2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% (w/v) polyethylene glycol 3350, 200mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.14 42.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.003 α = 90.98 b = 48.79 β = 97.34 c = 54.832 γ = 95.83
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 315r 2014-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97960 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.65 50 95.7 0.074 8.4 1.9 47801 45746
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.71 92.3 0.198 4.6 1.9
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 1ZIO 1.65 50 43435 2309 95.5 0.17747 0.17534 0.1859 0.2186 0.2275 RANDOM 18.729
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] -1.1 -0.01 -0.59 0.39 -0.09 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_4_deg 17.802 r_dihedral_angle_3_deg 13.105 r_long_range_B_refined 7.602 r_long_range_B_other 7.551 r_dihedral_angle_1_deg 5.331 r_scangle_other 5.113 r_scbond_it 3.355 r_scbond_other 3.355 r_angle_other_deg 2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.032 r_dihedral_angle_4_deg 17.802 r_dihedral_angle_3_deg 13.105 r_long_range_B_refined 7.602 r_long_range_B_other 7.551 r_dihedral_angle_1_deg 5.331 r_scangle_other 5.113 r_scbond_it 3.355 r_scbond_other 3.355 r_angle_other_deg 2.4 r_mcangle_other 2.275 r_mcangle_it 2.271 r_angle_refined_deg 2.246 r_mcbond_it 1.67 r_mcbond_other 1.657 r_chiral_restr 0.134 r_bond_refined_d 0.021 r_gen_planes_other 0.013 r_gen_planes_refined 0.012 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 3369 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement