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X-ray structure of the adduct formed between hen egg white lysozyme and NAMI-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4J1A PDB entry 4J1A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 Crystals of the HEWL/NAMI-A adduct suitable for X-ray diffraction studies Have been grown by hanging drop vapor diffusion by mixing 1 L of 20 mg/mL HEWL/NAMI-A complex (protein to metal ratio 1:10) with an equal volume of reservoir solution containing 1.0 M NaCl and 50 mM sodium acetate pH 4.5. These crystals were fished with nylon loops and flash-frozen at 100 K using nitrogen gas, without cryoprotectant. This procedure partly dehydrates the crystals, enhancing in some cases the resolution of X-ray diffraction data, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 37.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.772 α = 90 b = 77.772 β = 90 c = 37.316 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 RIGAKU SATURN 944+ mirrors 2013-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 1.85 22.15 98.9 0.095 5.3 5.3 10143 10143
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 4J1A 1.85 22.15 9628 490 98.91 0.17933 0.17626 0.1845 0.23994 0.2412 RANDOM 26.913
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] -0.2 -0.2 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.814 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_4_deg 14.15 r_long_range_B_refined 7.92 r_long_range_B_other 7.77 r_dihedral_angle_1_deg 5.974 r_scangle_other 5.475 r_scbond_it 3.63 r_scbond_other 3.628 r_mcangle_it 2.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.814 r_dihedral_angle_3_deg 14.422 r_dihedral_angle_4_deg 14.15 r_long_range_B_refined 7.92 r_long_range_B_other 7.77 r_dihedral_angle_1_deg 5.974 r_scangle_other 5.475 r_scbond_it 3.63 r_scbond_other 3.628 r_mcangle_it 2.912 r_mcangle_other 2.911 r_mcbond_it 2.244 r_mcbond_other 2.227 r_angle_refined_deg 1.768 r_angle_other_deg 0.961 r_chiral_restr 0.115 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1000 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement CNS refinement CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling CNS phasing