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Crystal structure of Notothenia coriiceps adenylate kinase variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 200mM lithium sulfate, 100mM acetate pH4.0, 41% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.7 54.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.435 α = 90 b = 105.435 β = 90 c = 83.753 γ = 90
Symmetry Space Group P 41 21 2
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 270 2017-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
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 99.9 0.09 24.9 7.1 37833
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 1.97 100 0.781 7.1
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 5X6K 1.9 50 35880 1841 99.88 0.17663 0.17489 0.1892 0.21138 0.2205 RANDOM 27.778
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] -0.13 -0.13 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.606 r_dihedral_angle_4_deg 15.52 r_dihedral_angle_3_deg 13.821 r_long_range_B_refined 7.307 r_long_range_B_other 7.273 r_scangle_other 6.279 r_dihedral_angle_1_deg 5.831 r_scbond_it 4.134 r_scbond_other 4.132 r_mcangle_other 3.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.606 r_dihedral_angle_4_deg 15.52 r_dihedral_angle_3_deg 13.821 r_long_range_B_refined 7.307 r_long_range_B_other 7.273 r_scangle_other 6.279 r_dihedral_angle_1_deg 5.831 r_scbond_it 4.134 r_scbond_other 4.132 r_mcangle_other 3.251 r_mcangle_it 3.246 r_mcbond_it 2.434 r_angle_refined_deg 2.421 r_mcbond_other 2.421 r_angle_other_deg 0.951 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2876 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 119
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing