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Structure of DNA-free long form XPD from Thermoplasma acidophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VSF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 1M Sodium Potassium tartrate, 0.2M Sodium Chloride, 0.1M bis-Tris Propane pH 7
Crystal Properties Matthews coefficient Solvent content 3.06 59.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.53 α = 90 b = 96 β = 90 c = 159.09 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2024-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11583 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.11 159.09 99.1 0.16 0.999 11.2 12.8 52613
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.11 2.18 89.4 0.5405 0.091 9.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.127 12.822 51761 2530 99.401 0.204 0.202 0.2028 0.245 0.2452 RANDOM 69.538
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] 3.088 -2.102 -0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.402 r_dihedral_angle_6_deg 15.289 r_lrange_it 11.458 r_lrange_other 11.451 r_dihedral_angle_2_deg 9.872 r_dihedral_angle_1_deg 8.577 r_scangle_other 8.525 r_scangle_it 8.519 r_mcangle_it 6.425 r_mcangle_other 6.424
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.402 r_dihedral_angle_6_deg 15.289 r_lrange_it 11.458 r_lrange_other 11.451 r_dihedral_angle_2_deg 9.872 r_dihedral_angle_1_deg 8.577 r_scangle_other 8.525 r_scangle_it 8.519 r_mcangle_it 6.425 r_mcangle_other 6.424 r_scbond_other 5.457 r_scbond_it 5.453 r_mcbond_it 4.261 r_mcbond_other 4.261 r_angle_refined_deg 2.026 r_angle_other_deg 0.944 r_nbd_refined 0.168 r_nbtor_refined 0.151 r_symmetry_nbd_other 0.117 r_symmetry_nbd_refined 0.11 r_chiral_restr 0.108 r_xyhbond_nbd_refined 0.089 r_nbd_other 0.075 r_symmetry_nbtor_other 0.061 r_symmetry_xyhbond_nbd_refined 0.027 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5040 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing