☰ Navigation Tabs
Crystal Structure of Bacteriophytochrome chromophore binding domain at 1.45 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZTU pdb entry 1ZTU without chromophore or his tag
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 0.095 M sodium citrate, 19% v/v isopropanol, 19% v/v PEG 4000, 5% V/V glycerol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.333 α = 90 b = 51.75 β = 116.29 c = 80.437 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2005-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 5ID-B APS 5ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 20 97.5 0.039 12.6 3.7 58316 56868 -3
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 1.45 1.5 83.3 0.276 3 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 1ZTU without chromophore or his tag 1.45 19.55 56866 54013 2853 97.47 0.1664 0.16503 0.1711 0.19204 0.1993 RANDOM 24.157
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] -0.7 -0.2 0.96 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 18.882 r_dihedral_angle_3_deg 13.739 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.63 r_angle_refined_deg 1.842 r_scbond_it 1.792 r_mcangle_it 1.182 r_mcbond_it 0.785 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.664 r_dihedral_angle_4_deg 18.882 r_dihedral_angle_3_deg 13.739 r_dihedral_angle_1_deg 5.725 r_scangle_it 2.63 r_angle_refined_deg 1.842 r_scbond_it 1.792 r_mcangle_it 1.182 r_mcbond_it 0.785 r_nbtor_refined 0.315 r_nbd_refined 0.237 r_symmetry_hbond_refined 0.235 r_xyhbond_nbd_refined 0.214 r_symmetry_vdw_refined 0.201 r_chiral_restr 0.118 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2403 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction