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CRYSTAL STRUCTURE OF MONOMERIC BACTERIOPHYTOCHROME mutant D207L Y263F From Synchrotron
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S7Q 3S7Q, 4O8G experimental model PDB 4O8G 3S7Q, 4O8G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 Crystals of D207L-Y263F phytochrome mutant were grown from hanging drop vapor diffusion in 20% PEG400, starting protein concentration of 20 mg/ml, and 0.1M phosphate citrate buffer at pH 4.0.
Crystal Properties Matthews coefficient Solvent content 2.23 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.434 α = 90 b = 53.34 β = 90.91 c = 65.69 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2015-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9785 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.3 23.8 96.5 0.052 33.2 7.7 77741 8.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 94.3 0.35 1 7.7
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 MOLECULAR REPLACEMENT THROUGHOUT 3S7Q, 4O8G 1.3 23.22 73911 3829 96.36 0.14531 0.14455 0.1458 0.16019 0.1618 RANDOM 16.698
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] -0.47 -0.71 0.59 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.835 r_sphericity_free 21.125 r_dihedral_angle_4_deg 12.679 r_dihedral_angle_3_deg 12.353 r_dihedral_angle_1_deg 6.383 r_sphericity_bonded 4.376 r_long_range_B_refined 1.778 r_long_range_B_other 1.479 r_angle_refined_deg 1.314 r_scangle_other 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.835 r_sphericity_free 21.125 r_dihedral_angle_4_deg 12.679 r_dihedral_angle_3_deg 12.353 r_dihedral_angle_1_deg 6.383 r_sphericity_bonded 4.376 r_long_range_B_refined 1.778 r_long_range_B_other 1.479 r_angle_refined_deg 1.314 r_scangle_other 1.05 r_rigid_bond_restr 0.968 r_scbond_it 0.945 r_scbond_other 0.944 r_mcangle_it 0.884 r_mcangle_other 0.884 r_angle_other_deg 0.871 r_mcbond_it 0.752 r_mcbond_other 0.751 r_chiral_restr 0.069 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2389 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing