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Crystal structure of Repressor from Salmonella-temperate phage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.2 296 15%(w/v) PEG 4000, 0.1M magnesium sulfate
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.599 α = 89.99 b = 62.497 β = 89.97 c = 267.896 γ = 72.7
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 ADSC QUANTUM 270 2015-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97935 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.98 50 98.6 22.8 1.6 75973
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 5D50 2.98 49.13 72158 3813 97.45 0.21855 0.21564 0.2328 0.27324 0.2826 RANDOM 77.309
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] 7.69 35.58 0.29 20.99 16.14 -28.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.58 r_dihedral_angle_3_deg 17.795 r_dihedral_angle_4_deg 17.16 r_long_range_B_refined 8.907 r_long_range_B_other 8.866 r_dihedral_angle_1_deg 7.465 r_mcangle_it 4.789 r_mcangle_other 4.789 r_scangle_other 3.746 r_mcbond_it 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.58 r_dihedral_angle_3_deg 17.795 r_dihedral_angle_4_deg 17.16 r_long_range_B_refined 8.907 r_long_range_B_other 8.866 r_dihedral_angle_1_deg 7.465 r_mcangle_it 4.789 r_mcangle_other 4.789 r_scangle_other 3.746 r_mcbond_it 2.83 r_mcbond_other 2.829 r_scbond_it 2.142 r_scbond_other 2.142 r_angle_refined_deg 1.254 r_angle_other_deg 0.842 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25435 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing HKL-2000 data scaling PHENIX phasing HKL-2000 data reduction