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Spatiotemporal development of soaked protein crystal; derivative 3610 sec
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LYM PDB ENTRY 2LYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH METHOD 4.5 293 25mg/ml Lysozyme, 0.05M SODIUM ACETATE, 0.7M SODIUM CHLORIDE, pH 4.5, BATCH METHOD, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.334 α = 90 b = 79.334 β = 90 c = 37.763 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 300 CCD MARMOSAIC 225 mm CCD 2013-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.07183 SPring-8 BL26B2
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 2 50 100 8604 8604 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 406
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 (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2LYM 2 50 8574 8571 403 99.97 0.18167 0.18167 0.17999 0.1799 0.21742 0.2159 RANDOM 22.794
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] -0.31 -0.31 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 22.537 r_dihedral_angle_3_deg 17.047 r_long_range_B_refined 7.347 r_dihedral_angle_1_deg 6.264 r_scbond_it 3.094 r_mcangle_it 2.68 r_mcbond_it 1.68 r_angle_refined_deg 1.514 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.625 r_dihedral_angle_4_deg 22.537 r_dihedral_angle_3_deg 17.047 r_long_range_B_refined 7.347 r_dihedral_angle_1_deg 6.264 r_scbond_it 3.094 r_mcangle_it 2.68 r_mcbond_it 1.68 r_angle_refined_deg 1.514 r_chiral_restr 0.116 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_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 66 Heterogen Atoms 3
Software Software Software Name Purpose BSS data collection REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling