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Catalytic domain of LPMO Lmo2467 from Listeria monocytogenes
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BEM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 297 Protein: 8.0 mg/ml, 0.01 M Tris HCl (pH 8.3); Screen: JCSG+ H9 (Qiagen),0.2 M AmSO4, 0.1 M Bis-Tris (pH 5.5), 25% (w/v) PEG3350.
Crystal Properties Matthews coefficient Solvent content 2.72 54.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.575 α = 90 b = 139.712 β = 90 c = 90.591 γ = 90
Symmetry Space Group C 2 2 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 MARMOSAIC 300 mm CCD 2016-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G .978 APS 21-ID-G
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 1.1 30 94.8 0.079 21.6 6.7 148923
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.12 66.9 0.749 1.6 3.9
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 2BEM 1.1 29.15 141504 7382 95.5 0.129 0.129 0.1288 0.145 0.1452 RANDOM 13.23
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] -0.3 -0.15 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.238 r_sphericity_free 27.415 r_dihedral_angle_4_deg 11.085 r_dihedral_angle_3_deg 9.951 r_dihedral_angle_1_deg 6.609 r_sphericity_bonded 6.34 r_long_range_B_refined 3.149 r_long_range_B_other 1.766 r_angle_refined_deg 1.428 r_rigid_bond_restr 0.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.238 r_sphericity_free 27.415 r_dihedral_angle_4_deg 11.085 r_dihedral_angle_3_deg 9.951 r_dihedral_angle_1_deg 6.609 r_sphericity_bonded 6.34 r_long_range_B_refined 3.149 r_long_range_B_other 1.766 r_angle_refined_deg 1.428 r_rigid_bond_restr 0.939 r_angle_other_deg 0.926 r_scangle_other 0.877 r_scbond_it 0.751 r_scbond_other 0.748 r_mcangle_it 0.699 r_mcangle_other 0.699 r_mcbond_it 0.525 r_mcbond_other 0.523 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 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 2534 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing