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Neutron Structure of PcyA D105N Mutant Complexed with Biliverdin at Room Temperature
X-RAY DIFFRACTION - NEUTRON DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3F0M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 NaCl, ammonium sulfate, MES
Crystal Properties Matthews coefficient Solvent content 2.74 55.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.174 α = 90 b = 97.523 β = 90 c = 43.277 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 PIXEL DECTRIS PILATUS3 2M 2021-06-06 M SINGLE WAVELENGTH 2 1 neutron 300 DIFFRACTOMETER iBIX 2021-03-20 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A 2 SPALLATION SOURCE J-PARC MLF BEAMLINE BL-03 2.63-6.06 JPARC MLF BL-03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (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 1.38 43.28 99.6 0.997 12.2 4.9 62402 15.07 2 2.1 21.16 99.3 0.9828 9.18 6.9377 18158 15.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.4 0.752 2 2.1 2.17 0.4789
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT 1.38 34.58 1.35 62359 1127 99.34 0.1505 0.1501 0.1523 0.1716 0.1733 17.93 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2.1 21.12 18158 98.6847 0.1657 0.1806
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 f_dihedral_angle_d 19.4914 f_angle_d 1.4608 f_chiral_restr 0.0921 f_bond_d 0.016 f_plane_restr 0.0117
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1925 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement REFMAC phasing