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Crystal structure of T4 Lysozyme V131C synthetic dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C6T PDB entry 1C6T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 295 20% PEG 8000, 0.1M Na Cacodylate, pH 6.5, 0.2M Ammonium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.27 45.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.267 α = 90 b = 29.408 β = 97.39 c = 31.243 γ = 90
Symmetry Space Group C 1 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 IMAGE PLATE RIGAKU RAXIS IV 2004-05-26 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 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 25 96.8 0.068 14.3 15287 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 93.5 0.445 2.05
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 1C6T 2 25 2 11299 10730 567 97.8 0.181 0.178 0.1802 0.24 0.2451 RANDOM 14.05
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] 0.63 0.27 -1.03 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.557 r_dihedral_angle_4_deg 18.283 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 5.937 r_scangle_it 5.015 r_scbond_it 3.437 r_mcangle_it 1.754 r_angle_refined_deg 1.715 r_mcbond_it 1.216 r_symmetry_vdw_refined 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.557 r_dihedral_angle_4_deg 18.283 r_dihedral_angle_3_deg 15.324 r_dihedral_angle_1_deg 5.937 r_scangle_it 5.015 r_scbond_it 3.437 r_mcangle_it 1.754 r_angle_refined_deg 1.715 r_mcbond_it 1.216 r_symmetry_vdw_refined 0.36 r_nbtor_refined 0.297 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.191 r_symmetry_hbond_refined 0.158 r_chiral_restr 0.127 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 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 1316 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing