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Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase, cobalt form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VCF
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
10% xylitol
5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.56 51.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.01 α = 90 b = 108.01 β = 90 c = 491.61 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 2019-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979364 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 2.3 50 99.8 0.143 0.998 10.59 8.8 142530 61
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 2.3 2.44 98.8 2.173 0.44 0.79
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 FOURIER SYNTHESIS THROUGHOUT 6VCF 2.3 49.44 135427 7076 99.78 0.2384 0.2376 0.2413 0.2538 0.2551 RANDOM 69.28
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] -0.65 -0.32 -0.65 2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.013 r_dihedral_angle_4_deg 15.221 r_dihedral_angle_3_deg 14.039 r_dihedral_angle_1_deg 8.022 r_angle_refined_deg 1.347 r_angle_other_deg 1.153 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.013 r_dihedral_angle_4_deg 15.221 r_dihedral_angle_3_deg 14.039 r_dihedral_angle_1_deg 8.022 r_angle_refined_deg 1.347 r_angle_other_deg 1.153 r_chiral_restr 0.052 r_bond_refined_d 0.006 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 21144 Nucleic Acid Atoms Solvent Atoms 460 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing