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The photosensory module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) in the Pr form, chromophore modelled with an endocyclic double bond in pyrrole ring A
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, HANGING DROP 8 298 16% PEG3350, 0.2 M CaCl2, 0.1 M Tris/HCl
Crystal Properties Matthews coefficient Solvent content 2.7 54.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.019 α = 90 b = 173.019 β = 90 c = 78.823 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 CCD ADSC QUANTUM 315r 2010-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9395 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 46.55 96.7 0.061 0.999 20 7.3 16105 62.1
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 2.7 2.85 87.7 0.64 3.3 6.1
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 5HSQ 2.7 46.55 15275 830 96.17 0.2187 0.21566 0.2123 0.27901 0.2795 RANDOM 77.119
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] 3.37 3.37 -6.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.991 r_dihedral_angle_4_deg 15.401 r_dihedral_angle_3_deg 15.251 r_dihedral_angle_1_deg 5.999 r_long_range_B_refined 4.544 r_long_range_B_other 4.522 r_mcangle_it 2.471 r_mcangle_other 2.471 r_scangle_other 2.368 r_angle_refined_deg 1.447
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.991 r_dihedral_angle_4_deg 15.401 r_dihedral_angle_3_deg 15.251 r_dihedral_angle_1_deg 5.999 r_long_range_B_refined 4.544 r_long_range_B_other 4.522 r_mcangle_it 2.471 r_mcangle_other 2.471 r_scangle_other 2.368 r_angle_refined_deg 1.447 r_scbond_it 1.441 r_scbond_other 1.44 r_mcbond_it 1.432 r_mcbond_other 1.432 r_angle_other_deg 0.942 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3558 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALEPACK data scaling PHASER phasing