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MecR1 unbound extracellular antibiotic-sensor domain.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XA1 PDB ENTRY 1XA1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 EQUIVOLUMETRIC HANGING DROPS CONSISTING OF 1.8M TRIBASIC AMMONIUM CITRATE AT PH7.0 AND PROTEIN SOLUTION AT 6.8MG/ML RENDERED CRYSTALS OF UNBOUND MECR1-PBD AT 20 DEGREES., pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.31 46.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.56 α = 90 b = 80.79 β = 90 c = 58.88 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 ESRF BM16
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 1.8 47.6 99.9 0.04 31.6 7.1 26121 1.5
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 1.8 1.9 100 0.18 10.5 7
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1XA1 1.8 47.6 25437 652 99.9 0.162 0.16 0.203 RANDOM 19.76
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] -1.05 1.58 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.202 r_dihedral_angle_4_deg 22.045 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_1_deg 6.038 r_scangle_it 4.59 r_scbond_it 2.896 r_mcangle_it 1.658 r_angle_refined_deg 1.647 r_mcbond_it 1.006 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.202 r_dihedral_angle_4_deg 22.045 r_dihedral_angle_3_deg 13.512 r_dihedral_angle_1_deg 6.038 r_scangle_it 4.59 r_scbond_it 2.896 r_mcangle_it 1.658 r_angle_refined_deg 1.647 r_mcbond_it 1.006 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.258 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.15 r_xyhbond_nbd_refined 0.141 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2093 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction COMBAT data scaling SCALA data scaling AMoRE phasing