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Crystal structure of mannitol operon repressor (MtlR) from Vibrio parahaemolyticus RIMD 2210633
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 289 0.2M tri-Ammonium citrate, 20% w/v PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.87 57.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.281 α = 90 b = 63.281 β = 90 c = 227.1 γ = 90
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 2007-02-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97927, 0.97941 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 2.75 48.56 99.2 0.1 17.5 4.8 23045 23045
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 2.75 2.83 91.6 0.642 1.5 2.7 1732
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.75 48.56 21778 21778 1178 99.14 0.21007 0.21007 0.20679 0.27272 0.2636 RANDOM 51.545
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] -0.13 -0.13 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.166 r_dihedral_angle_3_deg 24.867 r_dihedral_angle_4_deg 23.114 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.926 r_mcangle_it 1.853 r_scangle_it 1.725 r_mcbond_it 1.123 r_scbond_it 1.104 r_nbtor_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.166 r_dihedral_angle_3_deg 24.867 r_dihedral_angle_4_deg 23.114 r_dihedral_angle_1_deg 7.068 r_angle_refined_deg 1.926 r_mcangle_it 1.853 r_scangle_it 1.725 r_mcbond_it 1.123 r_scbond_it 1.104 r_nbtor_refined 0.337 r_nbd_refined 0.275 r_symmetry_vdw_refined 0.275 r_xyhbond_nbd_refined 0.169 r_chiral_restr 0.144 r_symmetry_hbond_refined 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5304 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXD phasing MLPHARE phasing DM phasing RESOLVE phasing HKL-3000 phasing