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Three-dimensional structure of s.aureus methicillin-resistance regulating transcriptional repressor meci in complex with 25-bp ds-DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 PEG 8000, magnesium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.6 α = 90 b = 133.6 β = 90 c = 54.7 γ = 120
Symmetry Space Group P 31 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID13 0.9789 ESRF ID13
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 2.8 39.7 97.8 0.089 19.7 3.5 14087 13777 86.5
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 2.8 2.9 93.6 0.5 2.3 2.9
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1OKR 2.8 39.7 13775 12877 898 97.81 0.21624 0.21624 0.21199 0.27601 RANDOM 31.56
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] -2.1 -1.05 -2.1 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.512 r_scangle_it 2.539 r_angle_refined_deg 1.938 r_scbond_it 1.613 r_mcangle_it 1.488 r_mcbond_it 0.765 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.512 r_scangle_it 2.539 r_angle_refined_deg 1.938 r_scbond_it 1.613 r_mcangle_it 1.488 r_mcbond_it 0.765 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.223 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2032 Nucleic Acid Atoms 1019 Solvent Atoms 37 Heterogen Atoms 1
Software Software Software Name Purpose XDS data scaling XSCALE data scaling AMoRE phasing REFMAC refinement XDS data reduction