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Human Pdrx5 complex with a ligand BP7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 291 22% PEG3350, 0.1M sodium citrate buffer (pH 5.3), 0.2M potassium sodium tartrate, 5mM 1,4-dithio-dl-threitol, 0.02%(w/v) sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.77 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.467 α = 90 b = 101.228 β = 90.09 c = 58.754 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 PSI PILATUS 6M 2013-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.07244 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.47 44.05 99.8 119074 2.3 2.1
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 (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 1.47 44.05 119074 6420 94.81 0.16383 0.16236 0.1696 0.19155 0.1931 RANDOM 13.948
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] -0.76 0.72 8.17 -7.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.221 r_dihedral_angle_4_deg 15.153 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 6.093 r_long_range_B_refined 3.745 r_long_range_B_other 3.745 r_angle_refined_deg 1.38 r_scangle_other 1.2 r_mcangle_it 0.991 r_mcangle_other 0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.221 r_dihedral_angle_4_deg 15.153 r_dihedral_angle_3_deg 14.47 r_dihedral_angle_1_deg 6.093 r_long_range_B_refined 3.745 r_long_range_B_other 3.745 r_angle_refined_deg 1.38 r_scangle_other 1.2 r_mcangle_it 0.991 r_mcangle_other 0.991 r_angle_other_deg 0.762 r_scbond_it 0.75 r_scbond_other 0.75 r_mcbond_it 0.599 r_mcbond_other 0.598 r_chiral_restr 0.079 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4784 Nucleic Acid Atoms Solvent Atoms 861 Heterogen Atoms 28
Software Software Software Name Purpose DNA data collection X-PLOR model building REFMAC refinement MOSFLM data reduction SCALA data scaling X-PLOR phasing