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BT984 a GH139 rhamnogalacturonan II exo-a-1,2-(2-Omethyl)-fucosidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model RoseTTAFold Unpublished structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 20 % PEG 3000
0.1 M Tris pH8.5
10 mg/ml
Crystal Properties Matthews coefficient Solvent content 2.6 52.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.201 α = 90 b = 138.322 β = 90 c = 195.53 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 PIXEL DECTRIS EIGER X 16M 2015-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9795 Diamond I04-1
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 2.7 47.478 98.9 0.997 10.4 3.3 75053
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 2.7 2.76 0.502 1.3
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.7 47.478 75016 3736 98.633 0.22 0.2182 0.2216 0.2557 0.2562 76.237
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] -5.108 -6.85 11.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.997 r_dihedral_angle_6_deg 14.23 r_lrange_it 11.478 r_lrange_other 11.478 r_mcangle_it 8.7 r_mcangle_other 8.7 r_scangle_it 8.68 r_scangle_other 8.679 r_dihedral_angle_2_deg 8.673 r_dihedral_angle_1_deg 6.968
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.997 r_dihedral_angle_6_deg 14.23 r_lrange_it 11.478 r_lrange_other 11.478 r_mcangle_it 8.7 r_mcangle_other 8.7 r_scangle_it 8.68 r_scangle_other 8.679 r_dihedral_angle_2_deg 8.673 r_dihedral_angle_1_deg 6.968 r_mcbond_it 5.664 r_mcbond_other 5.662 r_scbond_it 5.454 r_scbond_other 5.454 r_angle_refined_deg 1.4 r_angle_other_deg 0.504 r_symmetry_xyhbond_nbd_refined 0.344 r_xyhbond_nbd_other 0.251 r_nbd_other 0.249 r_nbd_refined 0.221 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.188 r_symmetry_nbd_refined 0.181 r_xyhbond_nbd_refined 0.146 r_ncsr_local_group_1 0.089 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.049 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12169 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing