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Hadesarchaea YNP_N21 cytochrome b5 domain protein (KUO41884.1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1J03
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 296.15 0.1M sodium citrate, 2M ammonium sulfate, pH 5.0
Crystal Properties Matthews coefficient Solvent content 1.99 38.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.17 α = 90 b = 72.17 β = 90 c = 22.81 γ = 120
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 EIGER X 16M 2018-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95370 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (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 1.9 23.62 100 0.179 0.183 0.04 15.8 20.7 5554
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.94 100 2.1 2.152 0.47 1.7 20.8
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 1J03 1.9 20 5262 280 99.87 0.22266 0.2206 0.229 0.26067 0.2655 RANDOM 28.629
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] -0.87 -0.44 -0.87 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.711 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_4_deg 14.84 r_dihedral_angle_1_deg 7.955 r_long_range_B_other 5.89 r_long_range_B_refined 5.832 r_scangle_other 4.132 r_mcangle_other 3.481 r_mcangle_it 3.471 r_scbond_it 2.621
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.711 r_dihedral_angle_3_deg 15.835 r_dihedral_angle_4_deg 14.84 r_dihedral_angle_1_deg 7.955 r_long_range_B_other 5.89 r_long_range_B_refined 5.832 r_scangle_other 4.132 r_mcangle_other 3.481 r_mcangle_it 3.471 r_scbond_it 2.621 r_scbond_other 2.565 r_angle_refined_deg 2.35 r_mcbond_it 2.214 r_mcbond_other 2.114 r_angle_other_deg 0.885 r_chiral_restr 0.058 r_bond_refined_d 0.01 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 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 599 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement