☰ Navigation Tabs
Crystal structure of pyrene-conjugated adenylate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AKE PDB ENTRY 1AKE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES sodium pH 7.5, 0.8M potassium sodium tartrate tetrahydrate', VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.114 α = 90 b = 58.992 β = 90 c = 118.308 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 RAYONIX MX-225 mirrors 2013-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.8 39.7 97.1 11218 11218 1.6 1.6 37.8
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 2.8 2.85 95.9 0.297
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1AKE 2.8 39.67 11218 10422 548 95.9 0.209 0.207 0.207 0.2065 0.256 0.2599 RANDOM 54.2
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] 16.69 -6 -10.69
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.81 c_mcangle_it 2.08 c_scbond_it 1.75 c_angle_deg 1.4 c_mcbond_it 1.2 c_improper_angle_d 0.99 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.5 c_scangle_it 2.81 c_mcangle_it 2.08 c_scbond_it 1.75 c_angle_deg 1.4 c_mcbond_it 1.2 c_improper_angle_d 0.99 c_bond_d 0.009 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3312 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 200
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling