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Real Time Reaction Intermediates in Stigmatella Bacteriophytochrome P2
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PTQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7 289 SaBphP2 (60 mg/mL) was mixed 3:2 with a solution containing 0.17 M Ammonium-acetate, 85 mmol/L sodium citrate, pH 6.5, 25.5 % PEG 4000, 15% glycerol, 3 % benzamidine hydrochloride.
Crystal Properties Matthews coefficient Solvent content 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.69 α = 90 b = 83.4 β = 107.63 c = 86.87 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 289 CCD MPCCD 2018-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.38 SACLA BL2
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 viscous jet injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30 5 8.9 (KeV)
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 4 (µl/min) undefined (µm) HPLC nuclear grade grease
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 20 100 0.96 0.094 15 543 38486
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 2.1 2.15 100 1.78 158
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 FOURIER SYNTHESIS THROUGHOUT 6PTQ 2.4 19.97 36327 1799 85.25 0.31412 0.31275 0.3156 0.34146 0.3618 RANDOM 24.071
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] 0.6 0.17 -0.2 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.249 r_dihedral_angle_3_deg 28.731 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_1_deg 13.059 r_long_range_B_refined 5.086 r_long_range_B_other 5.084 r_mcangle_it 2.695 r_mcangle_other 2.695 r_angle_refined_deg 2.211 r_scangle_other 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.249 r_dihedral_angle_3_deg 28.731 r_dihedral_angle_4_deg 20.551 r_dihedral_angle_1_deg 13.059 r_long_range_B_refined 5.086 r_long_range_B_other 5.084 r_mcangle_it 2.695 r_mcangle_other 2.695 r_angle_refined_deg 2.211 r_scangle_other 2.1 r_mcbond_it 1.689 r_mcbond_other 1.689 r_scbond_it 1.315 r_scbond_other 1.315 r_angle_other_deg 1.229 r_chiral_restr 0.271 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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 7320 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling