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HtxB D206A protein variant from Pseudomonas stutzeri in complex with hypophosphite to 1.12 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 290 0.1 M Bis-Tris pH 5.5 and 25 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.3 46.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.082 α = 90 b = 55.241 β = 90 c = 125.903 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 PIXEL DECTRIS PILATUS 6M 2017-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97951 Diamond I04
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 1.12 50.64 99.9 0.027 0.999 10.7 8.2 108281
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 1.12 1.139 98.7 1.59 0.322 0.4 4.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5ME4 1.12 50.64 102535 5337 99.6 0.16116 0.15984 0.1614 0.1867 0.1909 RANDOM 21.567
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] 1.14 -0.04 -1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.8 r_sphericity_free 24.536 r_sphericity_bonded 20.95 r_rigid_bond_restr 18.618 r_dihedral_angle_4_deg 18.334 r_dihedral_angle_3_deg 11.852 r_scbond_other 7.528 r_scbond_it 7.519 r_dihedral_angle_1_deg 6.337 r_scangle_other 6.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.8 r_sphericity_free 24.536 r_sphericity_bonded 20.95 r_rigid_bond_restr 18.618 r_dihedral_angle_4_deg 18.334 r_dihedral_angle_3_deg 11.852 r_scbond_other 7.528 r_scbond_it 7.519 r_dihedral_angle_1_deg 6.337 r_scangle_other 6.096 r_long_range_B_refined 4.743 r_long_range_B_other 4.742 r_mcbond_it 2.861 r_mcbond_other 2.861 r_mcangle_it 2.845 r_mcangle_other 2.784 r_angle_refined_deg 1.582 r_angle_other_deg 1.508 r_chiral_restr 0.084 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2033 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement TRUNCATE data reduction Aimless data scaling REFMAC phasing