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The structure of HtxB from Pseudomonas stutzeri in complex with hypophosphite to 1.52 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283 0.2 M Sodium/potassium tartrate, 0.1 M Bis-tris propane pH 8.5 and 20 % (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.24 α = 90 b = 55.21 β = 90 c = 125.2 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 2016-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.97951 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.52 22.81 97.7 0.117 0.998 9.8 7.1 42787
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 1.52 1.55 91.3 1.209 0.525 1.1 6
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 5JVB 1.52 22.8 40628 2115 97.52 0.1688 0.16732 0.1673 0.19771 0.1978 RANDOM 23.139
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] 1.11 -0.3 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.995 r_scbond_it 20.396 r_scbond_other 20.39 r_dihedral_angle_4_deg 19.739 r_scangle_other 15.464 r_long_range_B_other 15.108 r_long_range_B_refined 15.035 r_dihedral_angle_3_deg 13.171 r_dihedral_angle_1_deg 5.891 r_mcangle_it 4.725
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.995 r_scbond_it 20.396 r_scbond_other 20.39 r_dihedral_angle_4_deg 19.739 r_scangle_other 15.464 r_long_range_B_other 15.108 r_long_range_B_refined 15.035 r_dihedral_angle_3_deg 13.171 r_dihedral_angle_1_deg 5.891 r_mcangle_it 4.725 r_mcangle_other 4.724 r_mcbond_it 4.277 r_mcbond_other 4.075 r_angle_refined_deg 1.453 r_angle_other_deg 0.923 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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 2000 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing