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Crystal structure of SpGH92 in complex with mannose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 2.25 M (NH4)2SO4, 0.1M Bis-Tris
Crystal Properties Matthews coefficient Solvent content 3.47 64.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.003 α = 90 b = 161.711 β = 90 c = 208.404 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 ADSC QUANTUM 315r 2015-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.97531 SSRL BL7-1
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 2.15 127.76 99.9 0.103 14.4 7.5 237386
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 2WVY 2.15 127.76 225381 11855 99.89 0.198 0.1968 0.2029 0.2212 0.2278 RANDOM 35.789
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.229 r_dihedral_angle_4_deg 20.34 r_dihedral_angle_3_deg 13.383 r_dihedral_angle_1_deg 6.225 r_mcangle_it 3.118 r_mcbond_it 2.05 r_mcbond_other 2.048 r_angle_refined_deg 1.225 r_angle_other_deg 0.94 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.229 r_dihedral_angle_4_deg 20.34 r_dihedral_angle_3_deg 13.383 r_dihedral_angle_1_deg 6.225 r_mcangle_it 3.118 r_mcbond_it 2.05 r_mcbond_other 2.048 r_angle_refined_deg 1.225 r_angle_other_deg 0.94 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 21913 Nucleic Acid Atoms Solvent Atoms 1364 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction