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Crystal structure of MvfR ligand binding domain in complex with M64
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 31% MPD, 90 mM imidazole pH 8.0, 180mM MgCl2, 10mM Co(NH3)6Cl3
Crystal Properties Matthews coefficient Solvent content 4.15 70.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.556 α = 90 b = 121.524 β = 90 c = 112.757 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 2014-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.65 81.78 96.1 0.04 15.46 2.9 21542
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 2.65 2.9 95.2 0.438 2.38 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 4JVD 2.65 81.78 20678 863 96.46 0.2178 0.21637 0.2134 0.25113 0.2424 RANDOM 85.283
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] 4.34 2.16 -6.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_3_deg 15.224 r_dihedral_angle_4_deg 13.645 r_dihedral_angle_1_deg 6.563 r_scangle_it 4.982 r_scbond_it 3.452 r_mcangle_it 2.409 r_mcbond_it 1.896 r_angle_refined_deg 1.32 r_angle_other_deg 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.331 r_dihedral_angle_3_deg 15.224 r_dihedral_angle_4_deg 13.645 r_dihedral_angle_1_deg 6.563 r_scangle_it 4.982 r_scbond_it 3.452 r_mcangle_it 2.409 r_mcbond_it 1.896 r_angle_refined_deg 1.32 r_angle_other_deg 0.94 r_mcbond_other 0.308 r_symmetry_hbond_refined 0.205 r_symmetry_vdw_other 0.171 r_nbd_refined 0.17 r_nbtor_refined 0.16 r_nbd_other 0.136 r_symmetry_vdw_refined 0.118 r_xyhbond_nbd_refined 0.105 r_nbtor_other 0.077 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 3195 Nucleic Acid Atoms Solvent Atoms 17 Heterogen Atoms 74
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement REFMAC phasing