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Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, iron form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KVC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 22% Sokalan PA 25 CL
0.1 M MES-NaOH pH 6
0.1 M NaCl
22% Xylitol
Crystal Properties Matthews coefficient Solvent content 2.52 51.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.267 α = 90 b = 107.267 β = 90 c = 491.109 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2019-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979354 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.68 50 99.5 0.185 0.999 11.77 10.5 88233 66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.85 97.5 1.954 0.373 0.97 10.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3KVC 2.687 49.149 88143 4373 99.741 0.253 0.2516 0.2522 0.2714 0.2696 83.729
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] -0.846 -0.423 -0.846 2.744
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.277 r_dihedral_angle_4_deg 13.863 r_dihedral_angle_3_deg 12.868 r_dihedral_angle_1_deg 7.075 r_lrange_it 2.077 r_lrange_other 2.066 r_angle_refined_deg 1.198 r_angle_other_deg 1.051 r_mcangle_it 0.831 r_mcangle_other 0.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.277 r_dihedral_angle_4_deg 13.863 r_dihedral_angle_3_deg 12.868 r_dihedral_angle_1_deg 7.075 r_lrange_it 2.077 r_lrange_other 2.066 r_angle_refined_deg 1.198 r_angle_other_deg 1.051 r_mcangle_it 0.831 r_mcangle_other 0.831 r_scangle_it 0.493 r_scangle_other 0.493 r_mcbond_it 0.45 r_mcbond_other 0.45 r_scbond_it 0.267 r_scbond_other 0.267 r_symmetry_xyhbond_nbd_refined 0.211 r_nbd_refined 0.17 r_metal_ion_refined 0.162 r_nbtor_refined 0.159 r_nbd_other 0.157 r_symmetry_nbd_other 0.153 r_xyhbond_nbd_refined 0.131 r_symmetry_nbd_refined 0.11 r_ncsr_local_group_2 0.071 r_ncsr_local_group_1 0.068 r_symmetry_nbtor_other 0.067 r_ncsr_local_group_10 0.066 r_ncsr_local_group_7 0.062 r_ncsr_local_group_4 0.06 r_ncsr_local_group_13 0.059 r_ncsr_local_group_5 0.053 r_ncsr_local_group_3 0.052 r_ncsr_local_group_14 0.051 r_ncsr_local_group_9 0.048 r_ncsr_local_group_6 0.044 r_ncsr_local_group_8 0.044 r_ncsr_local_group_12 0.041 r_ncsr_local_group_11 0.04 r_ncsr_local_group_15 0.037 r_chiral_restr 0.036 r_xyhbond_nbd_other 0.032 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21385 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing