☰ Navigation Tabs
Crystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SR0 PDB ENTRY 3SR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291 A 1.5 UL SOLUTION CONTAINING 26 MG/ML OF PROTEIN, 20 MM MGCL2 AND 20 MM ADP IN 50 MM TRIS-HCL PH 7 WAS MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 5.6, 30% W/V PEG-4000 IN A 1:1 RATIO; VAPOR DIFFUSION; SITTING DROP; 291 K
Crystal Properties Matthews coefficient Solvent content 1.95 37.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.088 α = 90 b = 64.697 β = 90 c = 86.256 γ = 90
Symmetry Space Group P 21 21 21
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 2013-06-12 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 1.59 64.7 100 0.09 12.2 6.5 48649 3.1 15.53
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 1.59 1.64 100 0.62 3.1 6.7
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3SR0 1.594 40.265 1.34 48566 1030 99.94 0.1825 0.1817 0.1833 0.2158 0.2157 20.8
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 18.261 f_angle_d 1.328 f_chiral_restr 0.05 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3236 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 132
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction SCALA data scaling MOLREP phasing