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HtxB D206N protein variant from Pseudomonas stutzeri in a partially open conformation to 1.53 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ME4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 0.2 M ammonium sulphate, 0.1 M Bis-Tris pH 5.5 and 25 % (w/v) PEG
3350
Crystal Properties Matthews coefficient Solvent content 2.45 49.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.81 α = 90 b = 118.45 β = 90 c = 35.43 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 100 PIXEL DECTRIS PILATUS 6M 2018-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9718 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.53 43.47 99.9 0.017 0.999 19.1 6.7 45946
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.53 1.56 99.6 0.517 0.602 1.4 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ME4 1.53 45.43 43578 2288 99.82 0.1892 0.18787 0.21309 0.2336 RANDOM 32.344
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] 1.73 -1.25 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.377 r_dihedral_angle_4_deg 23.68 r_scbond_other 20.577 r_scbond_it 20.54 r_scangle_other 19.175 r_long_range_B_other 14.48 r_long_range_B_refined 14.478 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 6.761 r_mcangle_other 4.739
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.377 r_dihedral_angle_4_deg 23.68 r_scbond_other 20.577 r_scbond_it 20.54 r_scangle_other 19.175 r_long_range_B_other 14.48 r_long_range_B_refined 14.478 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 6.761 r_mcangle_other 4.739 r_mcangle_it 4.738 r_mcbond_it 4.33 r_mcbond_other 4.329 r_angle_refined_deg 1.463 r_angle_other_deg 0.986 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2070 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing