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C-terminal domain of EcoR124I HsdR subunit fused with the pH-sensitive GFP variant ratiometric pHluorin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 20% (w/v) PEG 3350, 0.2 M KH2PO4, 4% v/v acetone
Crystal Properties Matthews coefficient Solvent content 2.55 51.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.386 α = 90 b = 176.505 β = 90 c = 126.023 γ = 90
Symmetry Space Group C 2 2 21
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-F 2015-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 20 99.2 0.101 0.997 11.7 4.68 34464 41.27
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 2.59 97.4 0.51 2.74 4.63
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 1W7S 2.45 20 32725 1716 99.19 0.1949 0.19194 0.1954 0.25383 0.2563 RANDOM 39.959
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] 6.33 -2.99 -3.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.374 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 15.474 r_long_range_B_other 7.113 r_long_range_B_refined 7.108 r_dihedral_angle_1_deg 6.791 r_scangle_other 5.175 r_mcangle_it 4.771 r_mcangle_other 4.77 r_scbond_it 3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.374 r_dihedral_angle_4_deg 16.09 r_dihedral_angle_3_deg 15.474 r_long_range_B_other 7.113 r_long_range_B_refined 7.108 r_dihedral_angle_1_deg 6.791 r_scangle_other 5.175 r_mcangle_it 4.771 r_mcangle_other 4.77 r_scbond_it 3.29 r_scbond_other 3.289 r_mcbond_it 3.056 r_mcbond_other 3.054 r_angle_refined_deg 1.729 r_angle_other_deg 1.003 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 4810 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction MOLREP phasing