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X-ray crystallographic structure of Orf9b Apo Homodimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Z4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 1.2M Sodium Phosphate, 0.8M Potassium Phosphate, 0.2M Lithium Sulfate, and 0.1M Glycine pH 10.5
Crystal Properties Matthews coefficient Solvent content 3.04 59.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.28 α = 90 b = 75.28 β = 90 c = 80.21 γ = 120
Symmetry Space Group P 31 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 193.15 PIXEL DECTRIS PILATUS3 S 6M 2023-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.8 37.64 99.7 0.06155 0.06893 0.03073 0.998 11.49 4.9 12518 97.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.91 98.06 1.187 1.414 0.7572 0.319 0.93 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.8 37.64 1.36 12511 1248 99.7 0.2914 0.2856 0.2869 0.3414 0.3383 129.53
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.2418 f_angle_d 0.843 f_chiral_restr 0.0502 f_plane_restr 0.009 f_bond_d 0.0057
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1168 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing