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Benzene binding in the hydrophobic cavity of T4 lysozyme L99A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DMV PDB entry 3DMV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 277 2.0-2.2 M K/Na phosphate, pH 6.9, 5mM BME and 5mM oxidized BME. Complexes were prepared by soaking or vapor diffusion methods, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.003 α = 90 b = 60.003 β = 90 c = 95.732 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2005-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 53 98.3 18791 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 95.5
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 3DMV 1.8 45.69 17650 956 98.39 0.18313 0.18176 0.1832 0.20812 RANDOM 16.749
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] 0.14 0.07 0.14 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_3_deg 12.46 r_dihedral_angle_4_deg 10.414 r_dihedral_angle_1_deg 4.679 r_scangle_it 2.164 r_scbond_it 1.376 r_angle_refined_deg 0.974 r_mcangle_it 0.824 r_mcbond_it 0.52 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.801 r_dihedral_angle_3_deg 12.46 r_dihedral_angle_4_deg 10.414 r_dihedral_angle_1_deg 4.679 r_scangle_it 2.164 r_scbond_it 1.376 r_angle_refined_deg 0.974 r_mcangle_it 0.824 r_mcbond_it 0.52 r_nbtor_refined 0.294 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.171 r_symmetry_hbond_refined 0.13 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 1335 Nucleic Acid Atoms Solvent Atoms 254 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing