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Glycoside hydrolase BT_0986
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 15% (w/v) PEG 550 MME, 15% (w/v) PEG 20000, 0.25 M rahmnose, 50mM hepes
and 50 mm MOPS pH 7.56 6mM D-rhamnopyranose tetrazole
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.05 α = 90 b = 84.81 β = 99.2 c = 120.63 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 PILATUS 6M 2016-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 2.11 50.69 98.9 0.088 0.995 9.9 3.6 75602 1.5
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 2.11 2.16 98.9 0.818 0.548 1.5 3.6
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 (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 apo model 2.11 50.69 69011 3563 98.78 0.20064 0.1986 0.2036 0.24026 0.2382 RANDOM 41.332
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] -1.14 -1.24 0.48 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_4_deg 15.565 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 6.631 r_long_range_B_refined 3.984 r_long_range_B_other 3.984 r_scangle_other 2.595 r_mcangle_it 2.193 r_mcangle_other 2.193 r_scbond_it 1.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.175 r_dihedral_angle_4_deg 15.565 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 6.631 r_long_range_B_refined 3.984 r_long_range_B_other 3.984 r_scangle_other 2.595 r_mcangle_it 2.193 r_mcangle_other 2.193 r_scbond_it 1.549 r_scbond_other 1.549 r_angle_refined_deg 1.502 r_mcbond_it 1.336 r_mcbond_other 1.335 r_angle_other_deg 0.954 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 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 8271 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 62
Software Software Software Name Purpose xia2 data reduction Aimless data scaling MOLREP phasing Coot model building REFMAC refinement