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Ferredoxin NADP Oxidoreductase (Xfn)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JFC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.22 Magnesium Sulfate,
27% w/v Polyethylene glycol 3,350,
0.4% v/v Ethyl acetate
1 mM Sodium dithionite
Crystal Properties Matthews coefficient Solvent content 2.31 46.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.743 α = 90 b = 73.14 β = 96.73 c = 99.963 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 100 PIXEL DECTRIS PILATUS 6M 2016-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.95 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.55 39 98.8 0.1 7.7 4.2 25850 46.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.66 99.1 0.362 0.306 0.934 2.6 4.2
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 5JFC 2.55 39 25850 1226 98.6 0.186 0.183 0.2092 0.251 0.2737 RANDOM 44.63
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] 22.2376 -10.2418 6.9072 -29.1449
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.72 t_omega_torsion 3.08 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.72 t_omega_torsion 3.08 t_angle_deg 1.19 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5903 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 127
Software Software Software Name Purpose BUSTER refinement HKL-2000 data reduction Aimless data scaling PHENIX phasing