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Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at LCLS
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q0H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.95 283 sodium acetate, DTT, 2-methyl-2,4-pentandiol, PEG400
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.1 α = 90 b = 54.8 β = 92.6 c = 69.9 γ = 90
Symmetry Space Group C 1 2 1
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 CS-PAD CXI-1 2016-01-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.3 SLAC LCLS CXI
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 2.1 38.2 99.97 0.98 0.0919 7.77 819 20853
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4Q0H 2.1 38.2 18732 958 93.96 0.17811 0.1761 0.21827 0.2169 RANDOM 42.92
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] 0.56 -0.87 0.45 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.154 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_4_deg 10.703 r_dihedral_angle_1_deg 6.458 r_long_range_B_refined 5.963 r_long_range_B_other 5.963 r_scangle_other 3.405 r_mcangle_other 3.09 r_mcangle_it 3.088 r_scbond_it 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.154 r_dihedral_angle_3_deg 13.379 r_dihedral_angle_4_deg 10.703 r_dihedral_angle_1_deg 6.458 r_long_range_B_refined 5.963 r_long_range_B_other 5.963 r_scangle_other 3.405 r_mcangle_other 3.09 r_mcangle_it 3.088 r_scbond_it 2.022 r_scbond_other 2.021 r_mcbond_it 1.85 r_mcbond_other 1.83 r_angle_refined_deg 1.313 r_angle_other_deg 0.888 r_chiral_restr 0.065 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 2333 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling PHASER phasing