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The surface-engineered photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form with parallel dimer formation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 10-20% PEG4000, 100mM Tris buffer, 0.2M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.68 54.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.477 α = 90 b = 172.477 β = 90 c = 78.82 γ = 90
Symmetry Space Group I 4 2 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 PILATUS 6M 2015-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918410 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.42 46.49 99.94 0.999 22 8.6 22938
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.42 2.51 0.604
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 MOLECULAR REPLACEMENT THROUGHOUT 2.42 46.49 21783 1159 99.94 0.21408 0.21209 0.2135 0.25195 0.2568 RANDOM
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] -0.22 -0.22 0.44
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 6.785 r_long_range_B_refined 4.599 r_long_range_B_other 4.599 r_mcangle_other 3.071 r_mcangle_it 3.047 r_scangle_other 2.487 r_mcbond_other 2.098 r_mcbond_it 2.074 r_scbond_it 1.668 r_scbond_other 1.668
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 6.785 r_long_range_B_refined 4.599 r_long_range_B_other 4.599 r_mcangle_other 3.071 r_mcangle_it 3.047 r_scangle_other 2.487 r_mcbond_other 2.098 r_mcbond_it 2.074 r_scbond_it 1.668 r_scbond_other 1.668 r_bond_refined_d r_bond_other_d r_angle_refined_deg r_angle_other_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_chiral_restr r_gen_planes_refined r_gen_planes_other 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 3517 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling PHASER phasing XDS data reduction