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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 5I5L
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 30% PEG 3350 as cryoprotectant
Crystal Properties Matthews coefficient Solvent content 2.7 54.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 174.445 α = 90 b = 174.445 β = 90 c = 79.067 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 2006-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97952 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 3.11 46.84 99.3 0.083 0.093 0.041 0.997 16.3 9.4 11232 95.3
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 3.11 3.32 98.7 0.356 0.397 0.175 0.962 5 9.4
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 5I5L 3.11 46.84 10642 589 99.14 0.21895 0.21564 0.2208 0.27618 0.2706 RANDOM 103.842
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] 2.59 2.59 -5.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.292 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_1_deg 6.591 r_long_range_B_other 6.528 r_long_range_B_refined 6.525 r_scangle_other 3.977 r_mcangle_it 3.868 r_mcangle_other 3.867 r_scbond_it 2.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.292 r_dihedral_angle_3_deg 17.914 r_dihedral_angle_4_deg 16.777 r_dihedral_angle_1_deg 6.591 r_long_range_B_other 6.528 r_long_range_B_refined 6.525 r_scangle_other 3.977 r_mcangle_it 3.868 r_mcangle_other 3.867 r_scbond_it 2.438 r_scbond_other 2.438 r_mcbond_it 2.343 r_mcbond_other 2.341 r_angle_refined_deg 1.402 r_angle_other_deg 1.144 r_chiral_restr 0.043 r_bond_refined_d 0.004 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 3485 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building