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Crystal Structure of the alternate His 207 conformation of the Infrared Fluorescent D207H variant of Deinococcus Bacteriophytochrome chromophore binding domain at 2.45 angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9C PDB ENTRY 2O9C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 15% v/v PEG 4000, 20% v/v isopropanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.413 α = 90 b = 52.808 β = 113.13 c = 74.801 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 SMART 6000 Mirrors 2010-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.45 50 89.5 0.074 23 6.6 12893 11526 -3 56.5
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 2.45 2.49 37.5 0.452 1.45 2.3 246
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 (All) 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 2O9C 2.451 30.52 11553 10904 623 89.37 0.17772 0.17772 0.17423 0.1755 0.23644 0.2318 RANDOM 47.085
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] 0.44 1.9 -0.47 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.117 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 14.707 r_dihedral_angle_1_deg 6.085 r_scangle_it 2.348 r_mcangle_it 1.616 r_scbond_it 1.284 r_angle_refined_deg 1.245 r_mcbond_it 0.876 r_angle_other_deg 0.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.117 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 14.707 r_dihedral_angle_1_deg 6.085 r_scangle_it 2.348 r_mcangle_it 1.616 r_scbond_it 1.284 r_angle_refined_deg 1.245 r_mcbond_it 0.876 r_angle_other_deg 0.853 r_mcbond_other 0.078 r_chiral_restr 0.064 r_bond_refined_d 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2380 Nucleic Acid Atoms Solvent Atoms 163 Heterogen Atoms 43
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling