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Crystal structure of an S. thermophilus NFeoB E67A mutant bound to GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.8 298 0.1M ammonium acetate, 0.1M bis-tris(pH 6.0), 11%(w/v) PEG 10000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.6 α = 90 b = 92.1 β = 90 c = 206.8 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2010-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
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 2.5 50 98.5 0.085 16.6 4.8 43672 43672
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 2.5 2.54 98.3 0.548 2.5 4.5 2110
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 3LX8 2.5 47.09 42786 42786 2182 98.17 0.21915 0.21699 0.2121 0.25905 0.2523 RANDOM 47.12
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] 1.16 1.22 -2.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.832 r_dihedral_angle_4_deg 17.673 r_dihedral_angle_3_deg 14.025 r_dihedral_angle_1_deg 4.115 r_scangle_it 2.863 r_scbond_it 1.68 r_angle_refined_deg 1.403 r_mcangle_it 1.097 r_mcbond_it 0.582 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.832 r_dihedral_angle_4_deg 17.673 r_dihedral_angle_3_deg 14.025 r_dihedral_angle_1_deg 4.115 r_scangle_it 2.863 r_scbond_it 1.68 r_angle_refined_deg 1.403 r_mcangle_it 1.097 r_mcbond_it 0.582 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7908 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms 112
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling