☰ Navigation Tabs
Crystal structure of human adenylate kinase 4, AK4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BBW pdb entry 2BBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 sodium succinate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.738 α = 90 b = 95.514 β = 90 c = 140.873 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 225 mm CCD 2005-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.968 SLS X10SA
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 2.15 47.95 97.2 19.5 6.1 32401 32401
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.23 82.1 2.1 3.8 2704
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 2BBW 2.15 47.95 30746 30746 1635 97.14 0.16934 0.16934 0.16617 0.1752 0.22995 0.1679 RANDOM 23.47
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] -0.03 0.16 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.101 r_dihedral_angle_4_deg 17.241 r_dihedral_angle_3_deg 13.296 r_scangle_it 9.668 r_scbond_it 7.649 r_dihedral_angle_1_deg 6.118 r_mcangle_it 5.185 r_mcbond_it 4.212 r_angle_refined_deg 1.455 r_mcbond_other 1.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.101 r_dihedral_angle_4_deg 17.241 r_dihedral_angle_3_deg 13.296 r_scangle_it 9.668 r_scbond_it 7.649 r_dihedral_angle_1_deg 6.118 r_mcangle_it 5.185 r_mcbond_it 4.212 r_angle_refined_deg 1.455 r_mcbond_other 1.212 r_angle_other_deg 0.868 r_symmetry_vdw_refined 0.268 r_symmetry_vdw_other 0.225 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.192 r_nbd_other 0.178 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.116 r_nbtor_other 0.084 r_chiral_restr 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3470 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing