☰ Navigation Tabs
Crystal structure of Ser33 in complex with PHP (3-phosphohydroxypyruvate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M SPG pH=6
25 % w/v PEG 1500
7.4 mg/ml of protein in 25 mM Tris pH=7.5 and 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.85 56.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.6 α = 69.84 b = 95.15 β = 88.72 c = 108.37 γ = 85.65
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 PILATUS3 6M 2021-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9999 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 52.04 97.87 0.992 9.82 5.1 68361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.693 0.604 1.09
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 1YBA 2.6 52.04 64884 3369 97.93 0.22431 0.22237 0.2226 0.2617 0.2615 RANDOM 70.671
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] 1.29 6.11 -1.3 1.77 1.68 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.518 r_dihedral_angle_4_deg 18.987 r_dihedral_angle_3_deg 13.786 r_long_range_B_refined 10.996 r_long_range_B_other 10.995 r_mcangle_it 8.387 r_mcangle_other 8.386 r_scangle_other 8.34 r_dihedral_angle_1_deg 6.151 r_mcbond_other 5.663
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.518 r_dihedral_angle_4_deg 18.987 r_dihedral_angle_3_deg 13.786 r_long_range_B_refined 10.996 r_long_range_B_other 10.995 r_mcangle_it 8.387 r_mcangle_other 8.386 r_scangle_other 8.34 r_dihedral_angle_1_deg 6.151 r_mcbond_other 5.663 r_mcbond_it 5.662 r_scbond_it 5.548 r_scbond_other 5.545 r_angle_other_deg 1.151 r_angle_refined_deg 1.132 r_chiral_restr 0.035 r_bond_refined_d 0.007 r_bond_other_d 0.004 r_gen_planes_refined 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 12946 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 244
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing