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Wild-type PAS-GAF fragment from Deinococcus radiodurans Bphp collected at SACLA
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 VAPOR DIFFUSION, SITTING DROP 4.95 298 Sodium Acetate, Peg400, 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.57 52.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.22 α = 90 b = 55.49 β = 92.84 c = 71.63 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 CCD MPCCD 2015-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 0.987 SACLA BL3
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 2.2 71.54 100 0.976 0.119 5.62 81.2 18818
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 100 0.677 0.68 24.1
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 4Q0H 2.2 71.54 18389 956 100 0.18084 0.1821 0.1885 0.2033 0.2163 RANDOM 50.258
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] 0.36 -0.76 0.44 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.627 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_4_deg 12.759 r_long_range_B_refined 6.758 r_long_range_B_other 6.757 r_dihedral_angle_1_deg 6.216 r_scangle_other 4.406 r_mcangle_it 3.599 r_mcangle_other 3.599 r_scbond_it 2.593
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.627 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_4_deg 12.759 r_long_range_B_refined 6.758 r_long_range_B_other 6.757 r_dihedral_angle_1_deg 6.216 r_scangle_other 4.406 r_mcangle_it 3.599 r_mcangle_other 3.599 r_scbond_it 2.593 r_scbond_other 2.592 r_mcbond_it 2.196 r_mcbond_other 2.191 r_angle_refined_deg 1.287 r_angle_other_deg 0.913 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 2328 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction PHASER phasing CrystFEL data scaling