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Crystal structure of a substrate binding protein from Microbacterium hydrocarbonoxydans
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) PEG8000
Crystal Properties Matthews coefficient Solvent content 2.21 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.263 α = 90 b = 78.443 β = 90 c = 123.368 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 CCD RAYONIX MX225HE 2017-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9785 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 50 99.3 0.092 50.6 13.2 48691
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 95.7 1.1 2.8 11.5
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 1.75 39.551 48619 2397 99.133 0.195 0.1941 0.2033 0.2064 0.216 25.381
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] 0.104 0.409 -0.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.45 r_dihedral_angle_4_deg 15.541 r_dihedral_angle_3_deg 12.983 r_dihedral_angle_1_deg 10.518 r_lrange_it 4.535 r_lrange_other 4.498 r_scangle_it 3.528 r_scangle_other 3.528 r_mcangle_it 2.454 r_mcangle_other 2.454
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.45 r_dihedral_angle_4_deg 15.541 r_dihedral_angle_3_deg 12.983 r_dihedral_angle_1_deg 10.518 r_lrange_it 4.535 r_lrange_other 4.498 r_scangle_it 3.528 r_scangle_other 3.528 r_mcangle_it 2.454 r_mcangle_other 2.454 r_angle_other_deg 2.394 r_scbond_it 2.332 r_scbond_other 2.331 r_mcbond_it 1.657 r_mcbond_other 1.657 r_angle_refined_deg 1.465 r_symmetry_xyhbond_nbd_refined 0.213 r_symmetry_nbd_other 0.212 r_nbd_refined 0.198 r_nbd_other 0.174 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.14 r_symmetry_nbd_refined 0.122 r_symmetry_xyhbond_nbd_other 0.077 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.062 r_bond_other_d 0.037 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3546 Nucleic Acid Atoms Solvent Atoms 347 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELXD phasing