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Crystal structure of a lysozyme from Litopenaeus vannamei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LSY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298.15 HEPES 0.1M, pH 7.5, 20 (w/v) PEG 10,000%
Crystal Properties Matthews coefficient Solvent content 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.368 α = 90 b = 82.368 β = 90 c = 38.665 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 IMAGE PLATE RIGAKU Mirrors 2009-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.25 41.18 86.16 0.996 8.2 2.8 6270
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.32 0.993
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LSY 2.25 35.692 6270 622 86.162 0.204 0.1998 0.2068 0.2463 0.2518 23.065
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] -0.268 -0.134 -0.268 0.871
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.047 r_dihedral_angle_4_deg 22.238 r_dihedral_angle_3_deg 15.192 r_dihedral_angle_1_deg 7.681 r_lrange_it 5.68 r_lrange_other 5.654 r_scangle_it 3.16 r_scangle_other 3.158 r_mcangle_it 2.614 r_mcangle_other 2.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.047 r_dihedral_angle_4_deg 22.238 r_dihedral_angle_3_deg 15.192 r_dihedral_angle_1_deg 7.681 r_lrange_it 5.68 r_lrange_other 5.654 r_scangle_it 3.16 r_scangle_other 3.158 r_mcangle_it 2.614 r_mcangle_other 2.612 r_scbond_it 1.995 r_scbond_other 1.993 r_mcbond_it 1.66 r_mcbond_other 1.659 r_angle_refined_deg 1.527 r_angle_other_deg 1.382 r_nbd_refined 0.213 r_ext_dist_refined_d 0.198 r_symmetry_nbd_other 0.195 r_nbd_other 0.186 r_xyhbond_nbd_refined 0.181 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.11 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.068 r_symmetry_xyhbond_nbd_other 0.068 r_symmetry_nbd_refined 0.025 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1084 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing