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Neutron Structure of PcyA I86D 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 5B4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 ammonium sulfate, sodium chloride, sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.66 53.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.325 α = 90 b = 97.415 β = 90 c = 43.134 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 S 2M 2017-12-05 M SINGLE WAVELENGTH 2 1 neutron 300 IMAGE PLATE BIODIFF 2017-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A 2 NUCLEAR REACTOR FRM II BEAMLINE BIODIFF 3.1 FRM II BIODIFF
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 1.9 50 100 0.988 18.714 4.9 24473 26.18 2 2 55 84.2 0.9675 6.532 1.9 17734 26.18
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 1.9 1.93 0.797 2 2 2.05 0.762
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 1.9 36.91 1.35 24427 1999 99.74 0.1408 0.1378 0.1376 0.1741 0.1737 19.21 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 29.55 17648 84.1 0.1706 0.2029
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 28.8209 f_angle_d 1.4559 f_chiral_restr 0.0729 f_bond_d 0.016 f_plane_restr 0.0129
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1934 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 43
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing