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Crystal Structure of the Infrared Fluorescent D207H variant of Deinococcus Bacteriophytochrome chromophore binding domain at 1.72 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 14% v/v PEG 4000, 20% v/v isopropanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal Properties Matthews coefficient Solvent content 2.19 43.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.072 α = 90 b = 51.666 β = 115.33 c = 80.228 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 300 mm CCD mirrors 2010-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.9785 APS 21-ID-D
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 1.72 50 98.5 0.039 31.12 3.8 34268 33621 -3 18.8
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 1.72 1.75 97.3 0.215 5.53 3.5 1642
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 1.722 43.19 33564 31863 1701 97.92 0.16901 0.16901 0.16753 0.1723 0.19623 0.1997 RANDOM 21.053
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] -0.71 -0.08 0.48 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.795 r_dihedral_angle_4_deg 15.031 r_dihedral_angle_3_deg 11.693 r_dihedral_angle_1_deg 6.383 r_scangle_it 3.243 r_scbond_it 2.013 r_angle_refined_deg 1.479 r_mcangle_it 1.343 r_angle_other_deg 0.959 r_mcbond_it 0.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.795 r_dihedral_angle_4_deg 15.031 r_dihedral_angle_3_deg 11.693 r_dihedral_angle_1_deg 6.383 r_scangle_it 3.243 r_scbond_it 2.013 r_angle_refined_deg 1.479 r_mcangle_it 1.343 r_angle_other_deg 0.959 r_mcbond_it 0.742 r_mcbond_other 0.154 r_chiral_restr 0.078 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2395 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 43
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling