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Crystal of AmtR from Corynebacterium glutamicum in complex with DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 294 1.2 M Trisodium Citrate, 0.1 M NaHepes pH 6.8
Crystal Properties Matthews coefficient Solvent content 6.26 80.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.731 α = 90 b = 137.423 β = 90 c = 239.874 γ = 90
Symmetry Space Group P 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 2013-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 3 119.94 99 0.055 0.029 0.999 17.1 4.4 67304
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.07 99.8 0.683 0.358 0.774 2.1 4.6 4525
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5DY1 3 137.42 62963 3348 97.34 0.20677 0.2058 0.22398 0.2185 RANDOM 91.13
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] 7.98 -1.92 -6.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 19.058 r_dihedral_angle_3_deg 18.104 r_long_range_B_refined 16.561 r_long_range_B_other 16.561 r_scangle_other 12.957 r_mcangle_it 9.738 r_mcangle_other 9.737 r_scbond_it 8.468 r_scbond_other 8.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.744 r_dihedral_angle_4_deg 19.058 r_dihedral_angle_3_deg 18.104 r_long_range_B_refined 16.561 r_long_range_B_other 16.561 r_scangle_other 12.957 r_mcangle_it 9.738 r_mcangle_other 9.737 r_scbond_it 8.468 r_scbond_other 8.464 r_mcbond_it 6.744 r_mcbond_other 6.743 r_dihedral_angle_1_deg 5.42 r_angle_refined_deg 1.385 r_angle_other_deg 1.223 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 6590 Nucleic Acid Atoms 2120 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing