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Structure of lysozyme prepared by the 'soak-and-freeze' method under 100 bar of krypton pressure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ8 PDB ENTRY 1LZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 10% (W/V) NACL, 0.1M NA ACETATE PH 4.8 25% (V/V) ETH-GLYCOL
Crystal Properties Matthews coefficient Solvent content 2.09 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.001 α = 90 b = 79.001 β = 90 c = 37.053 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 PIXEL DECTRIS PILATUS 6M MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.2 55.86 99.9 0.06 24.7 13.8 70048 4.65
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 1.2 1.27 99.4 0.54 4.65 13.7
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 1LZ8 1.2 55.86 35416 1798 99.93 0.11 0.10878 0.1115 0.13445 0.1374 RANDOM 16.126
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_sphericity_free 50.835 r_dihedral_angle_2_deg 35.121 r_dihedral_angle_4_deg 18.583 r_rigid_bond_restr 12.221 r_sphericity_bonded 11.687 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 6.328 r_angle_other_deg 3.947 r_scbond_it 3.086 r_angle_refined_deg 2.042
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 50.835 r_dihedral_angle_2_deg 35.121 r_dihedral_angle_4_deg 18.583 r_rigid_bond_restr 12.221 r_sphericity_bonded 11.687 r_dihedral_angle_3_deg 11.628 r_dihedral_angle_1_deg 6.328 r_angle_other_deg 3.947 r_scbond_it 3.086 r_angle_refined_deg 2.042 r_mcangle_it 1.919 r_mcbond_other 1.523 r_mcbond_it 1.521 r_chiral_restr 0.148 r_gen_planes_other 0.027 r_bond_refined_d 0.02 r_gen_planes_refined 0.013 r_bond_other_d 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_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 994 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing