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T4 lysozyme with C-terminal extension
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SX7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.6 277 0.9 M K2HPO4, 1.1 M NaH2PO4, pH 6.6, 0.25 M NaCl, 49.0 mM oxidized B mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.66 53.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.117 α = 90 b = 60.117 β = 90 c = 97.108 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 II 1997-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 20 98.4 0.075 0.075 52.7 7.5 19210 19210 14.76
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 92 0.214 0.214 14.5 7.4 1760
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1sx7 1.8 20 18987 18987 964 97.91 0.15013 0.15013 0.14845 0.1626 0.18173 0.1967 RANDOM 11.308
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] 0.17 0.09 0.17 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.203 r_dihedral_angle_4_deg 14.67 r_dihedral_angle_3_deg 10.944 r_dihedral_angle_1_deg 4.998 r_scangle_it 3.654 r_scbond_it 2.48 r_mcangle_it 1.321 r_angle_refined_deg 1.284 r_mcbond_it 1.053 r_angle_other_deg 0.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.203 r_dihedral_angle_4_deg 14.67 r_dihedral_angle_3_deg 10.944 r_dihedral_angle_1_deg 4.998 r_scangle_it 3.654 r_scbond_it 2.48 r_mcangle_it 1.321 r_angle_refined_deg 1.284 r_mcbond_it 1.053 r_angle_other_deg 0.804 r_symmetry_vdw_other 0.284 r_xyhbond_nbd_refined 0.256 r_mcbond_other 0.246 r_nbd_refined 0.231 r_symmetry_vdw_refined 0.191 r_nbd_other 0.183 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.177 r_nbtor_other 0.081 r_chiral_restr 0.071 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1282 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing