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Cph1 phytochrome PAS-GAF-PHY Y176H mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VEA Only the residues 4-313 experimental model PDB 2VEA Only the residues 331-443, and 488-514
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 293 0.3 M ammonium formate
0.1 M HEPES pH 6.9
18% (w/v) Sokalan CP7
Crystal Properties Matthews coefficient Solvent content 3.49 64.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.873 α = 90 b = 135.873 β = 90 c = 355.644 γ = 90
Symmetry Space Group P 43 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 100 PIXEL DECTRIS PILATUS3 6M 2020-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3.696 47.651 99.3 0.8 0.157 0.982 6.3 25.8 36339
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 3.696 3.791 97.2 3.702 0.743 0.398 1.2 24.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.696 47.651 36303 1760 99.078 0.268 0.2657 0.2644 0.3068 0.3029 114.078
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] -0.487 -0.487 0.975
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.402 r_dihedral_angle_6_deg 15.312 r_lrange_it 6.601 r_lrange_other 6.601 r_dihedral_angle_1_deg 6.37 r_dihedral_angle_2_deg 5.899 r_mcangle_it 3.354 r_mcangle_other 3.354 r_scangle_it 2.354 r_scangle_other 2.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.402 r_dihedral_angle_6_deg 15.312 r_lrange_it 6.601 r_lrange_other 6.601 r_dihedral_angle_1_deg 6.37 r_dihedral_angle_2_deg 5.899 r_mcangle_it 3.354 r_mcangle_other 3.354 r_scangle_it 2.354 r_scangle_other 2.354 r_mcbond_it 1.881 r_mcbond_other 1.881 r_angle_refined_deg 1.338 r_chiral_restr_other 1.222 r_scbond_it 1.204 r_scbond_other 1.204 r_angle_other_deg 0.844 r_symmetry_xyhbond_nbd_refined 0.443 r_symmetry_nbd_refined 0.368 r_nbd_other 0.32 r_symmetry_nbd_other 0.224 r_nbd_refined 0.22 r_ncsr_local_group_5 0.186 r_nbtor_refined 0.18 r_ncsr_local_group_1 0.18 r_ncsr_local_group_3 0.179 r_ncsr_local_group_4 0.174 r_ncsr_local_group_6 0.174 r_ncsr_local_group_2 0.164 r_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_other 0.123 r_symmetry_xyhbond_nbd_other 0.109 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_ext_dist_refined_b 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15506 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing