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Crystal structure of Juvenile hormone diol kinase JHDK-L2 from silkworm, Bombyx mori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 289 0.2M Potassium sodium tartrate tetrahydrate, 0.1M Sodium citrate tribasic dihyrate pH 5.6, 2 M Ammonium sulfate.
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.96 α = 90 b = 67.57 β = 90 c = 69.47 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 80 CCD ADSC QUANTUM 315r 2018-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 1.22 48.484 99.5 0.074 17.6 12.48 67534
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 1.22 1.25 99.5 1.304 2.1 12.1
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2CCM 1.22 39.5 67398 3427 99.3 0.183 0.183 0.2 0.199 17.25
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] 0.451 -0.031 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 24.819 r_dihedral_angle_3_deg 11.867 r_dihedral_angle_1_deg 5.026 r_scangle_other 4.948 r_scangle_it 4.934 r_scbond_other 3.45 r_scbond_it 3.446 r_mcangle_other 2.609 r_mcangle_it 2.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 24.819 r_dihedral_angle_3_deg 11.867 r_dihedral_angle_1_deg 5.026 r_scangle_other 4.948 r_scangle_it 4.934 r_scbond_other 3.45 r_scbond_it 3.446 r_mcangle_other 2.609 r_mcangle_it 2.602 r_angle_refined_deg 2.467 r_angle_other_deg 1.716 r_mcbond_it 1.665 r_mcbond_other 1.648 r_nbd_refined 0.249 r_nbd_other 0.232 r_nbtor_refined 0.203 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.142 r_metal_ion_refined 0.1 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other r_xyhbond_nbd_other 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_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 1515 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction Aimless data scaling MOLREP phasing