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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 5K2B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5 293 0.1 M sodium citrate pH 5.0, 32 % PEG 400, 75 mM sodium thocyanate
Crystal Properties Matthews coefficient Solvent content 2.59 52.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.3 α = 90 b = 180.3 β = 90 c = 142.6 γ = 90
Symmetry Space Group C 2 2 21
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 2016-08-16 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) CC (Half) 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 3.2 45 99.8 0.992 7.7 142.6 7702
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.2 3.28 98.32 0.423
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 5K2B 3.2 45 7702 1301 99.8 0.24786 0.24132 0.2537 0.28721 0.2921 RANDOM 107.47
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] 3.46 -3.1 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 16.548 r_dihedral_angle_3_deg 13.034 r_long_range_B_refined 12.834 r_long_range_B_other 12.826 r_mcangle_other 7.72 r_mcangle_it 7.718 r_scangle_other 7.173 r_mcbond_it 4.728 r_mcbond_other 4.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.894 r_dihedral_angle_4_deg 16.548 r_dihedral_angle_3_deg 13.034 r_long_range_B_refined 12.834 r_long_range_B_other 12.826 r_mcangle_other 7.72 r_mcangle_it 7.718 r_scangle_other 7.173 r_mcbond_it 4.728 r_mcbond_other 4.72 r_dihedral_angle_1_deg 4.658 r_scbond_it 4.266 r_scbond_other 4.265 r_angle_refined_deg 1.614 r_angle_other_deg 1.068 r_chiral_restr 0.058 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 2978 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement Cheetah data collection CrystFEL data scaling CrystFEL data reduction MOLREP phasing