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Crystal structure of an S. thermophilus NFeoB N11A mutant bound to mGDP
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 6 293 0.2M LiCl, 0.1M Mes, 20% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.1 α = 90 b = 63.8 β = 90 c = 265.2 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2010-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 50 99.3 0.068 24.9 6.2 43892 43892 23
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 1.85 1.88 93.4 0.379 2.5 3.3 2060
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 1.85 50 43738 43738 2197 99.17 0.17776 0.17568 0.1804 0.21612 0.2206 RANDOM 16.326
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] 0.43 0.15 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.42 r_dihedral_angle_4_deg 11.594 r_dihedral_angle_3_deg 11.03 r_dihedral_angle_1_deg 4.625 r_scangle_it 3.211 r_scbond_it 2.085 r_mcangle_it 1.952 r_angle_refined_deg 1.502 r_mcbond_it 1.179 r_angle_other_deg 1.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.42 r_dihedral_angle_4_deg 11.594 r_dihedral_angle_3_deg 11.03 r_dihedral_angle_1_deg 4.625 r_scangle_it 3.211 r_scbond_it 2.085 r_mcangle_it 1.952 r_angle_refined_deg 1.502 r_mcbond_it 1.179 r_angle_other_deg 1.013 r_mcbond_other 0.297 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4046 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 95
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling