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Structure of XPD from Thermoplasma acidophilum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2M MGCL2, 10-15% PEG 400, 0.1M SODIUM CITRATE PH5.6
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.89 α = 90 b = 78.89 β = 90 c = 174.04 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 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.9 63.63 100 0.07 8.89 3.98 13622
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.06 100 0.62 1.24 3.56
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 MAD THROUGHOUT NONE 2.9 20 12870 657 100 0.209 0.206 0.204 0.287 0.2878 RANDOM 54.04
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] -0.15 -0.08 -0.15 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.813 r_dihedral_angle_3_deg 17.612 r_dihedral_angle_4_deg 13.261 r_dihedral_angle_1_deg 6.004 r_scangle_it 2.979 r_scbond_it 1.903 r_mcangle_it 1.47 r_angle_refined_deg 0.925 r_mcbond_it 0.791 r_angle_other_deg 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.813 r_dihedral_angle_3_deg 17.612 r_dihedral_angle_4_deg 13.261 r_dihedral_angle_1_deg 6.004 r_scangle_it 2.979 r_scbond_it 1.903 r_mcangle_it 1.47 r_angle_refined_deg 0.925 r_mcbond_it 0.791 r_angle_other_deg 0.78 r_nbd_refined 0.201 r_nbtor_refined 0.182 r_nbd_other 0.168 r_symmetry_vdw_other 0.137 r_symmetry_vdw_refined 0.135 r_symmetry_hbond_refined 0.118 r_xyhbond_nbd_refined 0.117 r_nbtor_other 0.081 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4751 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling SHARP phasing