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Silver Metallated Hen Egg White Lysozyme at 1.35 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KAM PDB ENTRY 3KAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 5 mM silver(I) 3-hydroxybutyrate, 3% (w/v) sodium nitrate, 25% (v/v) ethylene glycol, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.99 38.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.798 α = 90 b = 77.798 β = 90 c = 37.629 γ = 90
Symmetry Space Group P 43 21 2
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 APEX II CCD 2011-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS MICROFOCUS 1.54
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 1.35 25.55 99.7 32.84 18.08 25991 25935
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 PDB ENTRY 3KAM 1.35 25.55 24429 1303 99.25 0.19348 0.19237 0.194 0.21451 0.2158 RANDOM 15.317
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.01 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 12.804 r_dihedral_angle_1_deg 5.553 r_sphericity_free 4.001 r_sphericity_bonded 2.818 r_scangle_it 2.782 r_scbond_it 2.393 r_rigid_bond_restr 1.923 r_mcangle_it 1.419
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.01 r_dihedral_angle_4_deg 19.991 r_dihedral_angle_3_deg 12.804 r_dihedral_angle_1_deg 5.553 r_sphericity_free 4.001 r_sphericity_bonded 2.818 r_scangle_it 2.782 r_scbond_it 2.393 r_rigid_bond_restr 1.923 r_mcangle_it 1.419 r_angle_refined_deg 1.175 r_mcbond_it 0.863 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.256 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.198 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.089 r_metal_ion_refined 0.067 r_bond_refined_d 0.008 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 38
Software Software Software Name Purpose APEX data collection PHASER phasing REFMAC refinement SAINT data reduction APEX data reduction