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Crystallographic superstructure of the photosensory core module (PAS-GAF-PHY) of the bacterial phytochrome Agp1 (AtBphP1) locked in a Pr-like state
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 7.8 291 20-23% PEG 3350, 50 mM NaCl and 100 mM Tris/Cl, in 20% Sucrose as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.6 52.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 240.218 α = 90 b = 240.218 β = 90 c = 160.515 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 2006-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9791 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.4 47.89 99.9 0.101 0.128 0.079 0.99 10.5 4.9 32444 68.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.58 100 0.438 0.557 0.341 0.87 3.5 5
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 3.4 47.89 29735 1578 96.41 0.25713 0.25497 0.2565 0.29701 0.3003 RANDOM 79.097
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] -0.65 -0.65 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.536 r_dihedral_angle_4_deg 17.904 r_dihedral_angle_3_deg 17.801 r_dihedral_angle_1_deg 6.951 r_long_range_B_refined 4.783 r_long_range_B_other 4.782 r_mcangle_it 2.221 r_mcangle_other 2.221 r_scangle_other 1.787 r_angle_refined_deg 1.443
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.536 r_dihedral_angle_4_deg 17.904 r_dihedral_angle_3_deg 17.801 r_dihedral_angle_1_deg 6.951 r_long_range_B_refined 4.783 r_long_range_B_other 4.782 r_mcangle_it 2.221 r_mcangle_other 2.221 r_scangle_other 1.787 r_angle_refined_deg 1.443 r_mcbond_it 1.243 r_mcbond_other 1.243 r_angle_other_deg 1.104 r_scbond_it 0.992 r_scbond_other 0.992 r_chiral_restr 0.045 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 13946 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building