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X-ray structure of hen egg-white lysozyme with poly(allyl amine)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LKR PDB ENTRY 1LKR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1% PAA, 1.0M sodium chloride, 0.1M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.93 36.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.94 α = 90 b = 76.94 β = 90 c = 37.331 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 Bruker DIP-6040 2008-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.900 SPring-8 BL44XU
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 1.18 18.66 95.1 0.061 4.8 68455
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) 1.18 1.2 82.3 0.109 3.6 2923
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LKR 1.18 18.66 33979 1791 95.9 0.20409 0.20305 0.22368 0.2436 RANDOM 10.554
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.635 r_dihedral_angle_3_deg 11.803 r_dihedral_angle_4_deg 11.331 r_dihedral_angle_1_deg 5.311 r_sphericity_free 1.4 r_scangle_it 1.278 r_sphericity_bonded 1.074 r_angle_refined_deg 0.998 r_scbond_it 0.948 r_mcangle_it 0.733
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.635 r_dihedral_angle_3_deg 11.803 r_dihedral_angle_4_deg 11.331 r_dihedral_angle_1_deg 5.311 r_sphericity_free 1.4 r_scangle_it 1.278 r_sphericity_bonded 1.074 r_angle_refined_deg 0.998 r_scbond_it 0.948 r_mcangle_it 0.733 r_rigid_bond_restr 0.704 r_mcbond_it 0.398 r_nbtor_refined 0.294 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.19 r_metal_ion_refined 0.107 r_xyhbond_nbd_refined 0.095 r_chiral_restr 0.082 r_symmetry_hbond_refined 0.073 r_bond_refined_d 0.005 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1064 Nucleic Acid Atoms Solvent Atoms 143 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing