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a GH76 family enzyme structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D4A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 0.1 M AMMONIUM NITRATE, PH 6.5, 20% PEG 3350
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.06 α = 90 b = 85.17 β = 90 c = 101.86 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 PILATUS 6M-F 2016-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97959 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 1.46 50.93 99.9 0.05 0.999 16.2 6.5 127095 1.4
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 1.46 1.5 99.6 0.531 1.4 5.8 9293
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 4d4a 1.46 50.93 127007 6317 99.86 0.12288 0.12067 0.1222 0.16524 0.1239 RANDOM 26.791
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] 0.5 -0.49 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.233 r_sphericity_free 26.007 r_dihedral_angle_4_deg 24.683 r_sphericity_bonded 15.387 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 5.395 r_scangle_other 4.833 r_long_range_B_refined 4.532 r_long_range_B_other 4.532 r_scbond_it 4.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.233 r_sphericity_free 26.007 r_dihedral_angle_4_deg 24.683 r_sphericity_bonded 15.387 r_dihedral_angle_3_deg 11.493 r_dihedral_angle_1_deg 5.395 r_scangle_other 4.833 r_long_range_B_refined 4.532 r_long_range_B_other 4.532 r_scbond_it 4.484 r_scbond_other 4.484 r_rigid_bond_restr 3.992 r_mcangle_it 3.308 r_mcangle_other 3.308 r_mcbond_it 3.153 r_mcbond_other 3.153 r_angle_refined_deg 1.741 r_angle_other_deg 1.08 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5341 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing