☰ Navigation Tabs
Crystal structure of SapF (an ATP-binding protein) from non-typeable Haemophilus influenzae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P45289-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 8.5 293 1.6 M Lithium Sulfate, 0.1 M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.479 α = 90 b = 132.479 β = 90 c = 166.671 γ = 120
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++ VariMax HF 2025-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54187
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 2.3 67.52 100 0.099 0.103 0.026 0.999 19.8 15.7 25206
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 0.537 0.556 0.14 0.95 15
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 AF-P45289-F1 2.3 67.52 23939 1234 99.87 0.18856 0.18574 0.1945 0.24134 0.2463 RANDOM 47.056
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] -0.31 -0.16 -0.31 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.273 r_dihedral_angle_2_deg 9.078 r_long_range_B_refined 8.578 r_long_range_B_other 8.569 r_dihedral_angle_1_deg 7.325 r_scangle_other 5.944 r_mcangle_it 4.391 r_mcangle_other 4.391 r_scbond_it 3.707 r_scbond_other 3.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.273 r_dihedral_angle_2_deg 9.078 r_long_range_B_refined 8.578 r_long_range_B_other 8.569 r_dihedral_angle_1_deg 7.325 r_scangle_other 5.944 r_mcangle_it 4.391 r_mcangle_other 4.391 r_scbond_it 3.707 r_scbond_other 3.706 r_mcbond_it 2.75 r_mcbond_other 2.749 r_angle_refined_deg 1.592 r_angle_other_deg 0.525 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 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 3938 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 24
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction