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Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans complexed with 4-hydroxybenzoate hydrazide
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M sodium acetate
0.1 M sodium cacodylate, pH 7.5
30% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.26 45.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.296 α = 90 b = 77.561 β = 90 c = 121.711 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 95 PIXEL DECTRIS EIGER X 4M 2018-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.1 Photon Factory BL-1A
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 2.2 50 98.9 0.203 0.993 13.4 5.5 25212
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 2.2 2.24 98.2 0.627 0.756 2.4 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.2 47.314 25168 1297 98.048 0.21 0.2086 0.2109 0.2297 0.2325 28.864
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] -0.455 0.574 -0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_4_deg 18.337 r_dihedral_angle_3_deg 15.707 r_dihedral_angle_1_deg 10.549 r_lrange_it 3.962 r_lrange_other 3.962 r_scangle_it 2.772 r_scangle_other 2.772 r_angle_other_deg 2.412 r_mcangle_it 2.369
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.967 r_dihedral_angle_4_deg 18.337 r_dihedral_angle_3_deg 15.707 r_dihedral_angle_1_deg 10.549 r_lrange_it 3.962 r_lrange_other 3.962 r_scangle_it 2.772 r_scangle_other 2.772 r_angle_other_deg 2.412 r_mcangle_it 2.369 r_mcangle_other 2.368 r_scbond_it 1.699 r_scbond_other 1.698 r_mcbond_it 1.471 r_mcbond_other 1.471 r_angle_refined_deg 1.464 r_nbd_other 0.338 r_symmetry_nbd_refined 0.323 r_symmetry_nbd_other 0.208 r_nbd_refined 0.186 r_nbtor_refined 0.154 r_xyhbond_nbd_refined 0.14 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.071 r_chiral_restr_other 0.056 r_bond_other_d 0.037 r_symmetry_xyhbond_nbd_other 0.014 r_bond_refined_d 0.006 r_gen_planes_other 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3537 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CRANK2 phasing