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Crystal structure of adenylate kinase ancestor 4 with Zn, Mg and Ap5A bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P3J PDB ENTRY 1P3J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 291 0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 4 AND 10 MM MGAP5A IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (100 MM SODIUM ACETATE PH 4.6, 50 MM MGCL2, 2M AMMONIUM SULFATE). CRYSTALS WERE GROWN BY SITTING DROP METHOD AT 18C.
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.999 α = 90 b = 73.999 β = 90 c = 100.782 γ = 90
Symmetry Space Group P 43 21 2
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 CCD 2014-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 ALS 8.2.1
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 1.54 59.65 88.1 0.06 23.8 13.1 37185 2
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 1.54 1.57 97.1 1.12 2 9.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1P3J 1.54 59.65 36242 866 88.02 0.15462 0.15356 0.1963 0.2171 RANDOM 26.5
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] 0.12 0.12 -0.24
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.652 r_dihedral_angle_2_deg 35.078 r_sphericity_bonded 26.59 r_dihedral_angle_3_deg 13.5 r_dihedral_angle_4_deg 10.699 r_dihedral_angle_1_deg 5.607 r_mcangle_it 3.13 r_scbond_it 2.863 r_mcbond_it 2.404 r_mcbond_other 2.387
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.652 r_dihedral_angle_2_deg 35.078 r_sphericity_bonded 26.59 r_dihedral_angle_3_deg 13.5 r_dihedral_angle_4_deg 10.699 r_dihedral_angle_1_deg 5.607 r_mcangle_it 3.13 r_scbond_it 2.863 r_mcbond_it 2.404 r_mcbond_other 2.387 r_rigid_bond_restr 1.886 r_angle_refined_deg 1.86 r_angle_other_deg 0.989 r_chiral_restr 0.1 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1657 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing