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Structure of engineered PyrR protein (PURPLE PyrR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A3C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 15% PEG 4000, 0.1 M Tris HCl pH 8.5, 0.2 M Magnesium Chloride
Crystal Properties Matthews coefficient Solvent content 2.63 53.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.15 α = 90 b = 77.15 β = 90 c = 286.77 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 2M 2013-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
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 2.5 53.59 99 10.9 11.9 29162
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) 2.5 2.61 1.166 2.4 12.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1a3c 2.5 74.5 29162 1546 98.72 0.20401 0.20159 0.25122 0.2252 RANDOM 50.048
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] 1.83 1.83 -3.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_4_deg 22.082 r_dihedral_angle_3_deg 20.778 r_long_range_B_refined 10.782 r_long_range_B_other 10.781 r_scangle_other 7.052 r_mcangle_it 6.166 r_mcangle_other 6.166 r_dihedral_angle_1_deg 5.782 r_scbond_it 4.516
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.833 r_dihedral_angle_4_deg 22.082 r_dihedral_angle_3_deg 20.778 r_long_range_B_refined 10.782 r_long_range_B_other 10.781 r_scangle_other 7.052 r_mcangle_it 6.166 r_mcangle_other 6.166 r_dihedral_angle_1_deg 5.782 r_scbond_it 4.516 r_scbond_other 4.516 r_mcbond_it 3.953 r_mcbond_other 3.951 r_angle_refined_deg 1.867 r_angle_other_deg 1.84 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_bond_other_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 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 5250 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing iMOSFLM data reduction