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Crystal structure of adenylate kinase ancestor 4 with Zn and AMP-ADP 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 7.5 291 0.5 UL OF PROTEIN MIXTURE (20 MG/ML ADK ANCESTOR 4 AND 20 MM MGADP IN 40 MM MOPS PH 7.0, 50 MM NACL, 2 MM TCEP) WAS MIXED WITH 0.5 UL OF MOTHER LIQUOR (0.1 M HEPES PH 7.5, 1.4 M SODIUM CITRATE TRIBASIC DIHYDRATE). CRYSTALS WERE GROWN BY SITTING DROP METHOD AT 18C.
Crystal Properties Matthews coefficient Solvent content 2.15 42.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.046 α = 90 b = 70.127 β = 103.78 c = 40.27 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 315 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 1.69 39.11 90.2 0.04 13.9 3.5 21392 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 1.69 1.72 87.1 0.5 2 3.4
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 1P3J 1.69 39.11 20393 979 90.12 0.16125 0.15774 0.1671 0.23376 0.2343 RANDOM 27.467
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] 0.08 0.03 -0.08 -0.01
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.009 r_dihedral_angle_2_deg 34.016 r_sphericity_bonded 22.739 r_dihedral_angle_3_deg 15.683 r_dihedral_angle_4_deg 14.661 r_dihedral_angle_1_deg 5.73 r_mcangle_it 3.655 r_scbond_it 3.239 r_mcbond_it 2.917 r_mcbond_other 2.893
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 45.009 r_dihedral_angle_2_deg 34.016 r_sphericity_bonded 22.739 r_dihedral_angle_3_deg 15.683 r_dihedral_angle_4_deg 14.661 r_dihedral_angle_1_deg 5.73 r_mcangle_it 3.655 r_scbond_it 3.239 r_mcbond_it 2.917 r_mcbond_other 2.893 r_rigid_bond_restr 2.071 r_angle_refined_deg 1.818 r_angle_other_deg 1.002 r_chiral_restr 0.096 r_bond_refined_d 0.014 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 1665 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing