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PAS-GAF fragment from Deinococcus radiodurans BphP assembled with BV - Y307S, high dose
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, SITTING DROP 5.6 296 10% PEG3350, 19% isopropanol, 5% glycerol, 100 mM citric acid/NaOH, ph 5.6
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.274 α = 90 b = 51.803 β = 116.22 c = 80.272 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 PIXEL DECTRIS PILATUS 6M 2013-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25
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 1.7 50 96.2 0.105 25 6.8 33245
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 1.7 1.74 76.7 0.459 1.8 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.7 50 33245 1761 96.19 0.14643 0.14298 0.1552 0.21393 0.2224 RANDOM 28.207
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] -0.49 0.24 0.56 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.283 r_sphericity_free 21.846 r_dihedral_angle_4_deg 19.197 r_dihedral_angle_3_deg 13.95 r_sphericity_bonded 13.881 r_scangle_other 6.917 r_long_range_B_refined 6.691 r_long_range_B_other 6.691 r_dihedral_angle_1_deg 6.431 r_scbond_it 6.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.283 r_sphericity_free 21.846 r_dihedral_angle_4_deg 19.197 r_dihedral_angle_3_deg 13.95 r_sphericity_bonded 13.881 r_scangle_other 6.917 r_long_range_B_refined 6.691 r_long_range_B_other 6.691 r_dihedral_angle_1_deg 6.431 r_scbond_it 6.187 r_scbond_other 6.186 r_rigid_bond_restr 6.052 r_mcangle_other 5.807 r_mcangle_it 5.801 r_mcbond_it 4.976 r_mcbond_other 4.95 r_angle_refined_deg 2.043 r_angle_other_deg 1.234 r_chiral_restr 0.127 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2403 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling