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The crystal structure of transcriptional regulator YaiJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 297 8% PEG8K, 0.1M NA Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.51 α = 90 b = 65.51 β = 90 c = 88.94 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2003-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 20 90.16 20550 20550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.795 75
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 MOLECULAR REPLACEMENT THROUGHOUT 1.75 20 19496 19496 1054 90.16 0.19464 0.19464 0.19396 0.2 0.20748 0.2153 RANDOM 27.068
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] 0.68 0.34 0.68 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.156 r_scangle_it 3.855 r_scbond_it 2.873 r_mcangle_it 1.366 r_angle_refined_deg 1.291 r_mcbond_it 0.664 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.156 r_scangle_it 3.855 r_scbond_it 2.873 r_mcangle_it 1.366 r_angle_refined_deg 1.291 r_mcbond_it 0.664 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.167 r_xyhbond_nbd_refined 0.156 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.08 r_bond_refined_d 0.02 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_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 1415 Nucleic Acid Atoms Solvent Atoms 122 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement CrystalClear data reduction CrystalClear data scaling AMoRE phasing