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Crystal structure of T4 Lysozyme D72C 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 VAPOR DIFFUSION, HANGING DROP 7 298 0.2 M tri-Lithium Citrate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.17 61.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.306 α = 90 b = 55.907 β = 108.13 c = 80.292 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 IMAGE PLATE RIGAKU 2006-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00000 ALS 8.2.2
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 2.1 76.25 99.5 27769 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) 2.1 2.18 98.8
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 2.35 52.6 2 19569 18576 993 99.67 0.24277 0.23939 0.237 0.30355 0.3012 RANDOM 21.3
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] 1.11 0.63 -1.86 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.825 r_dihedral_angle_3_deg 18.106 r_dihedral_angle_4_deg 16.462 r_dihedral_angle_1_deg 7.128 r_scangle_it 5.075 r_scbond_it 3.514 r_angle_refined_deg 2.08 r_mcangle_it 1.954 r_mcbond_it 1.478 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.825 r_dihedral_angle_3_deg 18.106 r_dihedral_angle_4_deg 16.462 r_dihedral_angle_1_deg 7.128 r_scangle_it 5.075 r_scbond_it 3.514 r_angle_refined_deg 2.08 r_mcangle_it 1.954 r_mcbond_it 1.478 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.297 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.193 r_chiral_restr 0.133 r_bond_refined_d 0.026 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 2612 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing