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Crystal Structure of a Monomeric Infrared Fluorescent Deinococcus radiodurans Bacteriophytochrome chromophore binding domain
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 4.2 298 3% v/v PEG 1000, 20% v/v ethanol, 6% v/v glycerol, 0.1M phosphate citrate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.129 α = 90 b = 55.072 β = 92.23 c = 69.969 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 2011-03-05 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 Sym 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 1.748 30 99.2 0.06 22.1 3.6 36722 36431
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.748 1.79 100 0.225 4.7 3.6
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 2O9C 1.748 27.65 36431 34609 1822 99.18 0.18881 0.18734 0.1768 0.21693 0.2048 RANDOM 18.75
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] -0.01 -0.1 0.04 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.417 r_dihedral_angle_4_deg 15.036 r_dihedral_angle_3_deg 12.202 r_dihedral_angle_1_deg 6.188 r_scangle_it 2.416 r_angle_refined_deg 1.552 r_scbond_it 1.42 r_mcangle_it 1.199 r_angle_other_deg 0.965 r_mcbond_it 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.417 r_dihedral_angle_4_deg 15.036 r_dihedral_angle_3_deg 12.202 r_dihedral_angle_1_deg 6.188 r_scangle_it 2.416 r_angle_refined_deg 1.552 r_scbond_it 1.42 r_mcangle_it 1.199 r_angle_other_deg 0.965 r_mcbond_it 0.64 r_chiral_restr 0.074 r_mcbond_other 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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 2364 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 103
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling