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Structure of human adenylate kinase 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK2 PDB ENTRY 1AK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.7 0.1 M BIS-TRIS PH=5.7, 28% PEG3350, pH 5.70
Crystal Properties Matthews coefficient Solvent content 2.6 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.042 α = 90 b = 49.26 β = 90 c = 127.001 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 MARRESEARCH 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 2.1 45 99.9 0.14 10.8 7.12 17233
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 2.1 2.2 100 0.58 3 6.98
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 1AK2 2.1 50 16279 895 100 0.198 0.194 0.1997 0.274 0.2755 RANDOM 26.91
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] -0.92 0.7 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.981 r_dihedral_angle_3_deg 16.996 r_dihedral_angle_4_deg 14.296 r_scangle_it 8.215 r_dihedral_angle_1_deg 6.84 r_scbond_it 5.97 r_mcangle_it 3.656 r_mcbond_it 2.444 r_angle_refined_deg 1.768 r_angle_other_deg 0.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.981 r_dihedral_angle_3_deg 16.996 r_dihedral_angle_4_deg 14.296 r_scangle_it 8.215 r_dihedral_angle_1_deg 6.84 r_scbond_it 5.97 r_mcangle_it 3.656 r_mcbond_it 2.444 r_angle_refined_deg 1.768 r_angle_other_deg 0.998 r_symmetry_hbond_refined 0.262 r_symmetry_vdw_other 0.255 r_nbd_refined 0.224 r_xyhbond_nbd_refined 0.212 r_nbd_other 0.199 r_symmetry_vdw_refined 0.184 r_nbtor_refined 0.176 r_chiral_restr 0.091 r_nbtor_other 0.09 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1666 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing