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Lysozyme (denatured by DCl and refolded)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YVB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 NaCl, ethylene glycol
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.816 α = 90 b = 78.816 β = 90 c = 36.8 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 IMAGE PLATE RIGAKU RAXIS VII 2015-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.8 100 100 82.7 13.4 11225
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 FREE R-VALUE 2YVB 1.8 55.73 10639 584 99.97 0.15203 0.15007 0.1624 0.18733 0.1875 RANDOM 17.749
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] -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.698 r_dihedral_angle_4_deg 20.15 r_dihedral_angle_3_deg 11.081 r_long_range_B_refined 6.372 r_long_range_B_other 6.37 r_dihedral_angle_1_deg 5.882 r_scangle_other 4.368 r_scbond_it 3.155 r_scbond_other 3.151 r_mcangle_other 2.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.698 r_dihedral_angle_4_deg 20.15 r_dihedral_angle_3_deg 11.081 r_long_range_B_refined 6.372 r_long_range_B_other 6.37 r_dihedral_angle_1_deg 5.882 r_scangle_other 4.368 r_scbond_it 3.155 r_scbond_other 3.151 r_mcangle_other 2.083 r_mcangle_it 2.079 r_angle_refined_deg 1.759 r_mcbond_it 1.545 r_mcbond_other 1.515 r_angle_other_deg 1.206 r_chiral_restr 0.134 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 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 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 137 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing