☰ Navigation Tabs
D335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RCN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 282 10 mg/mL protein in the buffer of 25 mM PH 8.0 and 300 mM NaCl was mixed with 0.1 M MES, pH 5.5, 23 % (w/v) PEG 10000 at 1:1 to grow apo crystal. Then the apo was soaked directly with 4MU-6S-GlcNAc powder for 11 min.
Crystal Properties Matthews coefficient Solvent content 2.14 42.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.026 α = 90 b = 67.002 β = 94.673 c = 192.803 γ = 90
Symmetry Space Group P 1 21 1
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 2020-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979150 SSRF BL18U1
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 2.05 19.716 99.2 0.107 0.998 9.1 6.6 130228
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 2.05 2.09 1.024 0.53 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3rcn 2.05 19.716 130225 6601 99.159 0.23 0.2285 0.2292 0.2585 0.2598 37.394
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] -0.66 -0.629 1.133 -0.365
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.925 r_dihedral_angle_4_deg 19.1 r_dihedral_angle_3_deg 14.38 r_dihedral_angle_1_deg 6.422 r_lrange_it 4.577 r_scangle_it 2.901 r_mcangle_it 2.53 r_scbond_it 1.859 r_mcbond_it 1.618 r_angle_refined_deg 0.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.925 r_dihedral_angle_4_deg 19.1 r_dihedral_angle_3_deg 14.38 r_dihedral_angle_1_deg 6.422 r_lrange_it 4.577 r_scangle_it 2.901 r_mcangle_it 2.53 r_scbond_it 1.859 r_mcbond_it 1.618 r_angle_refined_deg 0.944 r_nbtor_refined 0.306 r_symmetry_nbd_refined 0.264 r_nbd_refined 0.191 r_symmetry_xyhbond_nbd_refined 0.131 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.08 r_ncsr_local_group_4 0.071 r_ncsr_local_group_5 0.067 r_ncsr_local_group_2 0.065 r_ncsr_local_group_3 0.063 r_ncsr_local_group_6 0.062 r_ncsr_local_group_1 0.059 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16687 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction