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Mite-y Lysozyme: Vegemite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BLX PDB ENTRY 2BLX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 4.5 293 Crystals were obtained by counter diffusion in capillary tubes stuck into Vegemite., pH 4.5, LIQUID DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.289 α = 90 b = 79.289 β = 90 c = 37.889 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 293 CCD ADSC QUANTUM 210 2009-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.98 Australian Synchrotron MX1
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 1.4 39.7 98 0.055 35.7 18.6 23901
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) 1 1.4 1.48 87 0.454 6.1 13.3
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 PDB ENTRY 2BLX 1.4 31.39 22629 1224 97.89 0.16296 0.16164 0.1582 0.18851 0.1869 RANDOM 19.385
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.043 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 13.949 r_scangle_it 6.527 r_dihedral_angle_1_deg 6.059 r_scbond_it 4.006 r_mcangle_it 3.054 r_angle_refined_deg 2.645 r_mcbond_it 1.84 r_chiral_restr 0.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.043 r_dihedral_angle_4_deg 22.196 r_dihedral_angle_3_deg 13.949 r_scangle_it 6.527 r_dihedral_angle_1_deg 6.059 r_scbond_it 4.006 r_mcangle_it 3.054 r_angle_refined_deg 2.645 r_mcbond_it 1.84 r_chiral_restr 0.165 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 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_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 78 Heterogen Atoms 1
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling