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Crystal Structure of Bacteriophytochrome chromophore binding domain
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 45.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.5 α = 90 b = 51.5 β = 116.4 c = 80.8 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 BRUKER PROTEUM Bruker Montel mirrors 2005-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 2.15 24 96.4 0.104 10 6.2 18137 17484 -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 2.15 2.23 78.8 0.333 2.7 2.6
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 2.15 23.71 17459 16539 920 96.5 0.1911 0.18852 0.1944 0.23695 0.243 RANDOM 32.353
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] -1.15 -0.12 0.76 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_1_deg 6.274 r_scangle_it 3.003 r_scbond_it 1.917 r_angle_refined_deg 1.806 r_mcangle_it 1.268 r_mcbond_it 0.796 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.565 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_3_deg 14.453 r_dihedral_angle_1_deg 6.274 r_scangle_it 3.003 r_scbond_it 1.917 r_angle_refined_deg 1.806 r_mcangle_it 1.268 r_mcbond_it 0.796 r_nbtor_refined 0.3 r_symmetry_hbond_refined 0.249 r_symmetry_vdw_refined 0.217 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.101 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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 2394 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 43
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection HKL-2000 data reduction