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Crystal structure of small laccase Ssl1 from Streptomyces sviceus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CG8 PDB ENTRY 3CG8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 50 mM HEPES, pH 7.0, 1.0-1.3 M ammonium sulfate, 5-20 mM hexamminecobalt(III) chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.02 38.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.54 α = 90 b = 103.82 β = 90 c = 162.26 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 Toroidal mirror 2012-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9144 ESRF ID23-1
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 2.13 47.97 99.47 0.064 17.3 4.4 49647 49366 3 3
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 2.13 2.3 98.7 0.425 3.27 4.1 8896
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3CG8 2.2 47.97 3 49366 42528 2259 99.57 0.20913 0.20597 0.26803 0.238 RANDOM 29.895
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.872 r_dihedral_angle_4_deg 20.161 r_dihedral_angle_3_deg 17.786 r_dihedral_angle_1_deg 7.547 r_scangle_it 4.121 r_scbond_it 2.821 r_angle_refined_deg 1.837 r_mcangle_it 1.664 r_mcbond_it 0.966 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.872 r_dihedral_angle_4_deg 20.161 r_dihedral_angle_3_deg 17.786 r_dihedral_angle_1_deg 7.547 r_scangle_it 4.121 r_scbond_it 2.821 r_angle_refined_deg 1.837 r_mcangle_it 1.664 r_mcbond_it 0.966 r_chiral_restr 0.125 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6265 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms 13
Software Software Software Name Purpose EDNA data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling