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Crystal structure of refolded PHOU-like protein (gi 2983430) from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T72 pdb entry 1T72
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.094 α = 90 b = 85.094 β = 90 c = 62.825 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 ADSC QUANTUM 4 double Si(111) crystal 2004-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.9792 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3.23 48 99.3 0.109 0.109 14 12.2 8109 120
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.23 3.393 90 0.78 0.78 2.1 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 SAD + molecular replacement THROUGHOUT pdb entry 1T72 3.23 15 1 8109 7667 367 99.09 0.21596 0.21427 0.2037 0.24846 0.2323 RANDOM 128.948
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] -3.79 -1.89 -3.79 5.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.805 r_scangle_it 2.612 r_angle_refined_deg 1.422 r_scbond_it 1.395 r_mcangle_it 0.705 r_symmetry_hbond_refined 0.374 r_mcbond_it 0.318 r_symmetry_vdw_refined 0.307 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.805 r_scangle_it 2.612 r_angle_refined_deg 1.422 r_scbond_it 1.395 r_mcangle_it 0.705 r_symmetry_hbond_refined 0.374 r_mcbond_it 0.318 r_symmetry_vdw_refined 0.307 r_nbd_refined 0.26 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3358 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Blu-Ice data collection SCALEPACK data scaling MOLREP phasing SOLVE phasing PHENIX phasing