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T4 lysozyme M102E/L99A mutant with buried charge in apolar cavity--pyridine 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 6.5 277 30% PEG 8000, 0.14M magnesium/calcium sulfate, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.07 40.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.957 α = 90 b = 48.957 β = 90 c = 129.315 γ = 90
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 8.2.1 1.000 ALS 8.2.1
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 1.5 48.96 97.5 0.047 20 3.7 47402 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 1.5 1.55 99.5 0.463 3.8 3.6
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GUI 1.5 48.96 44992 2403 97.56 0.21344 0.21134 0.2155 0.2534 0.2565 RANDOM 29.654
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] 1.2 1.2 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.371 r_dihedral_angle_3_deg 14.979 r_dihedral_angle_4_deg 13.407 r_dihedral_angle_1_deg 5.291 r_scangle_it 3.933 r_scbond_it 2.64 r_angle_refined_deg 1.643 r_mcangle_it 1.579 r_mcbond_it 1.217 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.371 r_dihedral_angle_3_deg 14.979 r_dihedral_angle_4_deg 13.407 r_dihedral_angle_1_deg 5.291 r_scangle_it 3.933 r_scbond_it 2.64 r_angle_refined_deg 1.643 r_mcangle_it 1.579 r_mcbond_it 1.217 r_nbtor_refined 0.308 r_nbd_refined 0.216 r_xyhbond_nbd_refined 0.173 r_symmetry_vdw_refined 0.172 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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 2586 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 31
Software Software Software Name Purpose Blu-Ice data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling