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Structure of the PAS domain code by the LIC_11128 gene from Leptospira interrogans serovar Copenhageni Fiocruz, solved at wavelength 3.09 A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M BIS-Tris pH 5,5, 17% w/v PEG 10,000, and 0.1 M Ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.39 48.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.91 α = 90 b = 144.56 β = 90 c = 48.65 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 12M 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 3.09 Diamond I23
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 72.28 81.04 0.08298 0.08386 0.0117 0.998 41.69 49.2 12470 64.86
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 78.66 1.433 0.636 2.39
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 2.5 72.28 10829 549 81.11 0.24325 0.24152 0.2415 0.27653 0.2682 RANDOM 72.629
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] -1.77 0.43 1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.473 r_long_range_B_refined 10.623 r_long_range_B_other 10.621 r_scangle_other 8.673 r_dihedral_angle_2_deg 6.063 r_dihedral_angle_1_deg 6.035 r_mcangle_it 5.543 r_mcangle_other 5.543 r_scbond_it 5.482 r_scbond_other 5.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.473 r_long_range_B_refined 10.623 r_long_range_B_other 10.621 r_scangle_other 8.673 r_dihedral_angle_2_deg 6.063 r_dihedral_angle_1_deg 6.035 r_mcangle_it 5.543 r_mcangle_other 5.543 r_scbond_it 5.482 r_scbond_other 5.48 r_mcbond_it 3.898 r_mcbond_other 3.897 r_angle_refined_deg 0.656 r_angle_other_deg 0.243 r_chiral_restr 0.036 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2667 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling HKL2Map phasing