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Structure of chemically synthesized human lysozyme at 1 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JSF 1JSF, see ref. K. Harada, Y. abe, M. Muraki, Proteins, 1998, 30, 232.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.9 293 c 6 mg/mL, 60 mM LiCl, 1.25 mM Hepes, 15 mM sodium phosphate, 1.25 M NaCl , pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.92 35.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.261 α = 90 b = 61.133 β = 90 c = 32.851 γ = 90
Symmetry Space Group P 21 21 21
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 2006-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C
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 1.04 50 53675
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 1JSF, see ref. K. Harada, Y. abe, M. Muraki, Proteins, 1998, 30, 232. 1.04 20 50848 2721 97.35 0.13361 0.13257 0.1334 0.15222 0.1522 RANDOM 8.171
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] -0.37 0.22 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.339 r_dihedral_angle_4_deg 15.693 r_sphericity_free 14.635 r_dihedral_angle_3_deg 11.198 r_dihedral_angle_1_deg 6.625 r_sphericity_bonded 6.034 r_scangle_it 4.847 r_scbond_it 3.946 r_mcangle_it 3.288 r_mcbond_it 2.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.339 r_dihedral_angle_4_deg 15.693 r_sphericity_free 14.635 r_dihedral_angle_3_deg 11.198 r_dihedral_angle_1_deg 6.625 r_sphericity_bonded 6.034 r_scangle_it 4.847 r_scbond_it 3.946 r_mcangle_it 3.288 r_mcbond_it 2.853 r_rigid_bond_restr 2.076 r_angle_refined_deg 1.716 r_mcbond_other 1.556 r_angle_other_deg 1.111 r_symmetry_vdw_other 0.365 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.221 r_nbd_other 0.209 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.183 r_chiral_restr 0.113 r_symmetry_vdw_refined 0.089 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.005 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2061 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing