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Crystal Structure HEW Lysozyme processed with the CrystalDirect automated mounting and cryo-cooling technology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4B0D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Crystallization experiments were carried out at the High Throughput Crystallization Laboratory of the EMBL Grenoble Outstation (https://embl.fr/htxlab) using the sitting-drop vapour diffusion method and CrystalDirect plates . Crystallization experiments were set up with 100 nl of sample and 100 nl of crystallization solution on the inner surface of the films within a CrystalDirect plate with a Cartesian PixSys robot (Cartesian Technologies). The crystallization solution was 0.1 M sodium acetate, pH=4.6 and 1.25 M sodium chloride.
Crystal Properties Matthews coefficient Solvent content 2.02 39.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.801 α = 90 b = 78.801 β = 90 c = 37.267 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 2015-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-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 1.2 19.7 100 0.06 17.2 8.4 37274
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22
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 4b0d 1.2 19.7 35325 1896 99.92 0.17452 0.17308 0.1829 0.20102 0.2101 RANDOM 13.983
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] 0.26 0.26 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_sphericity_free 17.92 r_dihedral_angle_1_deg 15.912 r_dihedral_angle_3_deg 11.675 r_dihedral_angle_4_deg 9.846 r_sphericity_bonded 4.068 r_rigid_bond_restr 4.035 r_angle_other_deg 2.18 r_long_range_B_refined 2.062 r_angle_refined_deg 1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.364 r_sphericity_free 17.92 r_dihedral_angle_1_deg 15.912 r_dihedral_angle_3_deg 11.675 r_dihedral_angle_4_deg 9.846 r_sphericity_bonded 4.068 r_rigid_bond_restr 4.035 r_angle_other_deg 2.18 r_long_range_B_refined 2.062 r_angle_refined_deg 1.9 r_long_range_B_other 1.361 r_mcangle_other 0.766 r_mcangle_it 0.718 r_scangle_other 0.712 r_mcbond_it 0.66 r_scbond_it 0.644 r_scbond_other 0.568 r_mcbond_other 0.519 r_chiral_restr 0.108 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 977 Nucleic Acid Atoms Solvent Atoms 215 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing