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Crystal structure of mouse sperm C-type lysozyme-like protein 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LSG PDB entry 1LSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 100 mM Bis-Tris, 20% w/v PEG5000 MME, 20% ethanol
Crystal Properties Matthews coefficient Solvent content 1.88 34.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.592 α = 90 b = 136.592 β = 90 c = 33.315 γ = 120
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 ADSC QUANTUM 315 2005-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9795 APS 19-ID
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 2.15 50.01 99.9 0.11 17 4.8 19824 19790 -3
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 2.15 2.19 100 0.918 1.9 4.7
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 1LSG 2.15 50.01 18760 1030 99.84 0.18978 0.18821 0.1945 0.21747 0.2242 RANDOM 45.063
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] 0.4 0.2 0.4 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_3_deg 15.022 r_dihedral_angle_4_deg 14.035 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.116 r_long_range_B_other 6.113 r_scangle_other 3.478 r_mcangle_it 3.227 r_mcangle_other 3.226 r_scbond_it 2.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.594 r_dihedral_angle_3_deg 15.022 r_dihedral_angle_4_deg 14.035 r_dihedral_angle_1_deg 7.274 r_long_range_B_refined 6.116 r_long_range_B_other 6.113 r_scangle_other 3.478 r_mcangle_it 3.227 r_mcangle_other 3.226 r_scbond_it 2.165 r_scbond_other 2.165 r_mcbond_other 1.904 r_mcbond_it 1.903 r_angle_refined_deg 1.707 r_angle_other_deg 1.238 r_chiral_restr 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.007 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 3046 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling EPMR phasing