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Crystal Structure of Adenylate Kinase from Aquifex Aeolicus in complex with Ap5A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 298 25%(v/v) PEG MME 550, 0.1 M MES pH 6.5, 0.01 M Zinc Sulfate, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.611 α = 90 b = 68.611 β = 90 c = 85.479 γ = 120
Symmetry Space Group P 31 2 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 210 2004-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.0 NSLS X6A
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 1.9 50 99.6 0.092 9 4.8 18796
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 1.9 1.97 97.9 0.546 3.9 1819
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 1AKE 1.9 50 18667 1840 99.13 0.209 0.205 0.2037 0.243 0.2418 RANDOM 24.967
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] 0.21 0.11 0.21 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.666 r_dihedral_angle_3_deg 17.792 r_dihedral_angle_4_deg 17.706 r_dihedral_angle_1_deg 5.701 r_scangle_it 4.203 r_scbond_it 2.659 r_angle_refined_deg 1.83 r_mcangle_it 1.617 r_mcbond_it 1.111 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.666 r_dihedral_angle_3_deg 17.792 r_dihedral_angle_4_deg 17.706 r_dihedral_angle_1_deg 5.701 r_scangle_it 4.203 r_scbond_it 2.659 r_angle_refined_deg 1.83 r_mcangle_it 1.617 r_mcbond_it 1.111 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.299 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.165 r_metal_ion_refined 0.125 r_chiral_restr 0.113 r_symmetry_hbond_refined 0.113 r_symmetry_metal_ion_refined 0.022 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1618 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 61
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction AMoRE phasing