☰ Navigation Tabs
Crystal structure of dimethyllysine hen egg-white lysozyme in complex with sclx4 at 1.9 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IPQ PDB ENTRY 4IPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.1 293.15 6 % PEG 8000, 100 mM, MAGNESIUM CHLORIDE, 50 mM SODIUM CHLORIDE, 100 mM SODIUM CACODYLATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal Properties Matthews coefficient Solvent content 2.23 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.85 α = 90 b = 30.2 β = 96.31 c = 94.21 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 198.8 CCD MARMOSAIC 225 mm CCD 2012-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.674 31.22 92 0.116 6.8 3.5 30169 27755 2.5 11.5
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 1.7 86.4 1.026 1.1 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4IPQ 1.9 31.2 19591 18582 1008 94.6 0.17 0.168 0.1683 0.21 0.2122 RANDOM 14.45
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] -0.06 -0.2 -0.53 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.612 r_dihedral_angle_4_deg 15.619 r_dihedral_angle_3_deg 12.975 r_dihedral_angle_1_deg 5.743 r_mcangle_it 1.272 r_angle_refined_deg 1.194 r_scbond_it 0.983 r_mcbond_it 0.744 r_chiral_restr 0.089 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.612 r_dihedral_angle_4_deg 15.619 r_dihedral_angle_3_deg 12.975 r_dihedral_angle_1_deg 5.743 r_mcangle_it 1.272 r_angle_refined_deg 1.194 r_scbond_it 0.983 r_mcbond_it 0.744 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it 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 2030 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 228
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement MOSFLM data reduction Aimless data scaling