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Crystal structure of putative transcriptional regulator LysR From Vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M MES Na pH 6.5, 0.8 M Magnesium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.87 34.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.291 α = 90 b = 83.11 β = 90 c = 95.509 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 2007-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97980 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 1.64 62.75 99.5 0.07 31.9 8.6 46907 45578 20.532
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 1.64 1.7 99.8 0.39 3.7 8.7 4635
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 1.64 62.75 44335 44335 2367 98.99 0.20625 0.20625 0.2045 0.2027 0.23982 0.2376 RANDOM 23.283
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] -0.52 -0.43 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.317 r_dihedral_angle_4_deg 17.288 r_dihedral_angle_3_deg 14.933 r_dihedral_angle_1_deg 8.562 r_scangle_it 3.13 r_scbond_it 2.086 r_angle_refined_deg 1.526 r_mcangle_it 1.506 r_mcbond_it 0.958 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.317 r_dihedral_angle_4_deg 17.288 r_dihedral_angle_3_deg 14.933 r_dihedral_angle_1_deg 8.562 r_scangle_it 3.13 r_scbond_it 2.086 r_angle_refined_deg 1.526 r_mcangle_it 1.506 r_mcbond_it 0.958 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.233 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.2 r_symmetry_hbond_refined 0.139 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 2982 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling MLPHARE phasing