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Crystal Structure of the Putative Transcriptional Regualator, MarR family from Porphyromonas gingivalis W83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1M HEPES pH 7.5, 1.4M sodium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.43 64.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.971 α = 90 b = 82.241 β = 90 c = 116.601 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315 mirrors 2005-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97948 APS 19-ID
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 2.15 38.78 92.9 0.071 13.7 10.9 18680 18091
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 2.15 2.23 69.3 0.254 4.76 8.8 1334
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.16 38.78 16189 16189 1851 92.84 0.2078 0.2078 0.20317 0.1986 0.25004 0.2463 RANDOM 59.765
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] 0.14 0.89 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.255 r_dihedral_angle_3_deg 19.877 r_dihedral_angle_4_deg 13.675 r_dihedral_angle_1_deg 6.007 r_scangle_it 2.428 r_scbond_it 1.529 r_angle_refined_deg 1.289 r_mcangle_it 1.015 r_mcbond_it 0.696 r_symmetry_hbond_refined 0.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.255 r_dihedral_angle_3_deg 19.877 r_dihedral_angle_4_deg 13.675 r_dihedral_angle_1_deg 6.007 r_scangle_it 2.428 r_scbond_it 1.529 r_angle_refined_deg 1.289 r_mcangle_it 1.015 r_mcbond_it 0.696 r_symmetry_hbond_refined 0.228 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.205 r_xyhbond_nbd_refined 0.195 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1669 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-2000 data reduction HKL-2000 data scaling SHARP phasing