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N-terminal PAS domain homodimer of PpANR MAP3K from Physcomitrella patens.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 290 2% PEG 500, 0.1M Tris base, 2.5M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.148 α = 90 b = 64.93 β = 121.4 c = 51.85 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS PILATUS3 6M KB mirrors 2015-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
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 1.7 40.17 98.9 0.059 12 3.7 26146 15.5
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 1.7 1.73 91.7 0.387 2.4 2.8
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 3LYX 1.7 40.16 24822 1322 98.32 0.16279 0.16091 0.1719 0.19847 0.2054 RANDOM 22.638
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] 1.47 0.12 1.41 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 13.393 r_long_range_B_refined 6.219 r_long_range_B_other 6.218 r_dihedral_angle_1_deg 5.958 r_scangle_other 4.202 r_mcangle_other 2.943 r_mcangle_it 2.939 r_scbond_it 2.678
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.919 r_dihedral_angle_4_deg 20.573 r_dihedral_angle_3_deg 13.393 r_long_range_B_refined 6.219 r_long_range_B_other 6.218 r_dihedral_angle_1_deg 5.958 r_scangle_other 4.202 r_mcangle_other 2.943 r_mcangle_it 2.939 r_scbond_it 2.678 r_scbond_other 2.678 r_mcbond_it 1.872 r_mcbond_other 1.852 r_angle_refined_deg 1.613 r_angle_other_deg 0.871 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1699 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement PHASER phasing Aimless data scaling xia2 data reduction