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Crystal structure of the cypemycin decarboxylase CypD.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 50 mM NaCl, 0.1 M Imidazole, 10 mM Tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 6.06 75.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.456 α = 90 b = 229.456 β = 90 c = 229.456 γ = 90
Symmetry Space Group F 41 3 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 PIXEL DECTRIS PILATUS3 S 6M 2017-10-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.6 50 100 0.182 0.044 26.8 18.7 16495
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.844 0.196 0.92 3.58 19.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD FREE R-VALUE 2.6 44.2 15611 831 99.94 0.17469 0.1724 0.1924 0.2193 0.2385 RANDOM 49.259
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.177 r_dihedral_angle_4_deg 22.066 r_dihedral_angle_3_deg 17.641 r_scangle_other 10.467 r_mcangle_it 9.72 r_mcangle_other 9.716 r_long_range_B_other 9.569 r_long_range_B_refined 9.568 r_scbond_it 9.374 r_scbond_other 9.372
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.177 r_dihedral_angle_4_deg 22.066 r_dihedral_angle_3_deg 17.641 r_scangle_other 10.467 r_mcangle_it 9.72 r_mcangle_other 9.716 r_long_range_B_other 9.569 r_long_range_B_refined 9.568 r_scbond_it 9.374 r_scbond_other 9.372 r_mcbond_it 8.119 r_mcbond_other 8.101 r_dihedral_angle_1_deg 7.174 r_rigid_bond_restr 4.236 r_angle_refined_deg 2.001 r_angle_other_deg 1.447 r_chiral_restr 0.099 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1359 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing