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Crystal structure of lysozyme with Keggin molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L PDB ENTRY 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 2-10% (M/V) NACL AND 0.1 M ACETATE BUFFER PH 4.5 (THE PROTEIN:WELL SOLUTION RATIO IN THE DROP WAS 1:1 WITH THE FINAL DROP VOLUME OF 4 MICROLITER USING A PROTEIN STOCK CONCENTRATION OF AROUND 50 MG/ML.
Crystal Properties Matthews coefficient Solvent content 1.91 35.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.96 α = 90 b = 77.96 β = 90 c = 36.41 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 160 CCD ADSC QUANTUM 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.67 30.38 99.6 0.02 29.7 13.5 13544 -1
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 1.67 1.76 100 0.1 6.4 13.4
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 193L 1.67 30.38 12793 667 99.48 0.21501 0.21249 0.2187 0.26664 0.2724 RANDOM 22.674
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] -1.47 -1.47 2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.837 r_dihedral_angle_4_deg 20.704 r_dihedral_angle_3_deg 14.229 r_dihedral_angle_1_deg 7.299 r_scangle_it 4.522 r_scbond_it 2.999 r_mcangle_it 1.891 r_angle_refined_deg 1.84 r_mcbond_it 1.194 r_angle_other_deg 1.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.837 r_dihedral_angle_4_deg 20.704 r_dihedral_angle_3_deg 14.229 r_dihedral_angle_1_deg 7.299 r_scangle_it 4.522 r_scbond_it 2.999 r_mcangle_it 1.891 r_angle_refined_deg 1.84 r_mcbond_it 1.194 r_angle_other_deg 1.184 r_mcbond_other 0.375 r_chiral_restr 0.12 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 987 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing