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Crystal structure of an AA10 LPMO from Photorhabdus luminescens
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 5.6 294 precipitant: 0.1 M sodium acetate (pH 5.2), 0.7 M 1,6-hexanediol
protein solution: holo-PlAA10 (10 mg/mL) in 50 mM MES (pH 6.5), 0.5 mM CuSO4
Crystal Properties Matthews coefficient Solvent content 2.38 48.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.53 α = 90 b = 80.39 β = 90 c = 90.91 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 2018-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
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 1.6 58.55 95.2 0.078 1 9.5 3.6 72679 14.6170167548
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 1.6 1.657 99.7 0.547 0.8 2.1 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2BEM 1.6000030918 58.5468363761 1.34347860769 70875 3556 95.0181657305 0.189634216194 0.188107113498 0.2002 0.218069528656 0.2293 19.9297799847
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 f_dihedral_angle_d 14.9887638647 f_angle_d 0.880813158622 f_chiral_restr 0.0557442998569 f_bond_d 0.00612783192797 f_plane_restr 0.00532827277765
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4126 Nucleic Acid Atoms Solvent Atoms 751 Heterogen Atoms 6
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing