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Crystal structure of Nitrosotalea devanaterra carotenoid cleavage dioxygenase in complex with 3-hydroxy-beta-apo-14'-carotenal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VCG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294.15 22% Sokalan PA 25 CL
0.1 M Mes-NaOH pH 6
0.1 M NaCl
13% Xylitol
5% glycerol
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.25 α = 90 b = 107.25 β = 90 c = 490.238 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 2019-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979356 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 2.35 50 99.9 0.13 0.999 12.83 10.6 131487 62
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 2.35 2.49 99.2 2.06 0.442 1.05
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 6VCG 2.35 49.13 124967 6518 99.86 0.214 0.2129 0.2178 0.2337 0.2359 RANDOM 76.413
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] 0.22 0.11 0.22 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.311 r_dihedral_angle_4_deg 15.103 r_dihedral_angle_3_deg 13.434 r_dihedral_angle_1_deg 8.06 r_angle_refined_deg 1.297 r_angle_other_deg 1.138 r_chiral_restr 0.048 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.311 r_dihedral_angle_4_deg 15.103 r_dihedral_angle_3_deg 13.434 r_dihedral_angle_1_deg 8.06 r_angle_refined_deg 1.297 r_angle_other_deg 1.138 r_chiral_restr 0.048 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21250 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing