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Crystal structure of lysozyme folded in SDS and 2-methyl-2,4-pentanediol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z55
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 300 100mM sodium acetate buffer pH 4.6 and 2M sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 1.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.595 α = 90 b = 77.595 β = 90 c = 37.567 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 CCD BRUKER PROTEUM 2005-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.3 34.7 99.7 0.082 21.9 8.1 5468
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) 2.3 100 0.022 8.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO THROUGHOUT 1Z55 2.3 34.7 5088 5195 244 99.72 0.20236 0.2018 0.214 0.2108 RANDOM 16.934
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] -0.32 -0.32 0.64
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 1083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.857 r_dihedral_angle_4_deg 22.302 r_dihedral_angle_3_deg 21.229 r_scangle_it 9.285 r_scbond_it 8.511 r_mcangle_it 6.421 r_dihedral_angle_1_deg 5.409 r_mcbond_it 4.122 r_angle_refined_deg 1.781 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.857 r_dihedral_angle_4_deg 22.302 r_dihedral_angle_3_deg 21.229 r_scangle_it 9.285 r_scbond_it 8.511 r_mcangle_it 6.421 r_dihedral_angle_1_deg 5.409 r_mcbond_it 4.122 r_angle_refined_deg 1.781 r_nbtor_refined 0.323 r_nbd_refined 0.265 r_symmetry_hbond_refined 0.254 r_symmetry_vdw_refined 0.253 r_xyhbond_nbd_refined 0.232 r_chiral_restr 0.07 r_bond_refined_d 0.028 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement SHELXL-97 refinement PROTEUM PLUS data reduction PROTEUM PLUS data scaling SHELX phasing SHELX model building