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Pentafluorobenzene 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 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.756 α = 90 b = 59.756 β = 90 c = 94.856 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 98.6 18531 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 91.6
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 45.41 17480 940 98.81 0.19403 0.1925 0.1938 0.22203 RANDOM 20.494
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] 0.25 0.12 0.25 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 12.415 r_dihedral_angle_3_deg 12.051 r_dihedral_angle_1_deg 4.95 r_scangle_it 2.123 r_scbond_it 1.361 r_angle_refined_deg 1.02 r_mcangle_it 0.904 r_mcbond_it 0.563 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.42 r_dihedral_angle_4_deg 12.415 r_dihedral_angle_3_deg 12.051 r_dihedral_angle_1_deg 4.95 r_scangle_it 2.123 r_scbond_it 1.361 r_angle_refined_deg 1.02 r_mcangle_it 0.904 r_mcbond_it 0.563 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.192 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.125 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 1346 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing