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T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--Benzene binding
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 30% PEG 8000, 0.2M ammounium sulfate, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.814 α = 90 b = 48.814 β = 90 c = 128.369 γ = 90
Symmetry Space Group P 41 21 2
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 315 Si(111) 2007-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.000 ALS 8.2.2
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 1.6 45.644 92.5 0.065 19.1 6 19653 2
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 1.6 1.66 96.2 0.398 3.9 6.2
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 3GUI 1.6 45.64 18627 1008 92.6 0.20425 0.20243 0.2015 0.23884 0.2411 RANDOM 25.532
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] -0.18 -0.18 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.758 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 4.977 r_scangle_it 2.86 r_scbond_it 1.854 r_angle_refined_deg 1.152 r_mcangle_it 1.031 r_mcbond_it 0.714 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.741 r_dihedral_angle_4_deg 18.758 r_dihedral_angle_3_deg 12.819 r_dihedral_angle_1_deg 4.977 r_scangle_it 2.86 r_scbond_it 1.854 r_angle_refined_deg 1.152 r_mcangle_it 1.031 r_mcbond_it 0.714 r_nbtor_refined 0.304 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.163 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1293 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement