☰ Navigation Tabs
Serial Millisecond Crystallography of Membrane and Soluble Protein Micro-crystals using Synchrotron Radiation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AVJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 6.5 293 0.1 M MES pH 6.5, 0.5 M sodium nitrate, 0.1 M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.01 43.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.3 α = 90 b = 68.3 β = 90 c = 108.2 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 298 PIXEL DECTRIS PILATUS3 6M 2016-08-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03 APS 23-ID-D
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 2.65 50.01 99.2 4.6 104.8 6769
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 5AVJ 2.65 50.01 6769 1095 99.17 0.22789 0.22541 0.2281 0.24269 0.2442 RANDOM 60.277
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] 0.18 0.18 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.314 r_dihedral_angle_4_deg 16.843 r_dihedral_angle_3_deg 11.356 r_long_range_B_refined 9.83 r_long_range_B_other 9.83 r_scangle_other 6.042 r_dihedral_angle_1_deg 5.784 r_mcangle_other 4.792 r_mcangle_it 4.79 r_scbond_it 3.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.314 r_dihedral_angle_4_deg 16.843 r_dihedral_angle_3_deg 11.356 r_long_range_B_refined 9.83 r_long_range_B_other 9.83 r_scangle_other 6.042 r_dihedral_angle_1_deg 5.784 r_mcangle_other 4.792 r_mcangle_it 4.79 r_scbond_it 3.966 r_scbond_other 3.87 r_mcbond_it 3.155 r_mcbond_other 3.146 r_angle_refined_deg 1.137 r_angle_other_deg 0.941 r_chiral_restr 0.06 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 2031 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling Coot model building MOLREP phasing Cheetah data collection