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Crystal structure of GDP-bound NFeoB from S. thermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LX5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 0.2M NaCl, 0.1M bis-Tris pH 5.5, 25% (w/v) PEG 3350, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.14 42.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.8 α = 90 b = 42.8 β = 90 c = 282.1 γ = 90
Symmetry Space Group P 41 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 IMAGE PLATE MAR 345 mm plate 2009-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5412
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 2.9 50 97.9 0.133 11.2 6.6 6494 6494 -3 -3 66.9
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 2.9 2.95 71.1 0.414 2 2.6 209
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 MOLECULAR REPLACEMENT THROUGHOUT 3LX5 2.9 50 -3 6427 6427 631 98.33 0.245 0.239 0.239 0.298 0.294 RANDOM 28.929
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] -2.55 -2.55 5.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_4_deg 13.349 r_dihedral_angle_1_deg 3.478 r_angle_refined_deg 1.494 r_scangle_it 1.287 r_mcangle_it 0.968 r_scbond_it 0.791 r_mcbond_it 0.525 r_chiral_restr 0.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.846 r_dihedral_angle_3_deg 15.198 r_dihedral_angle_4_deg 13.349 r_dihedral_angle_1_deg 3.478 r_angle_refined_deg 1.494 r_scangle_it 1.287 r_mcangle_it 0.968 r_scbond_it 0.791 r_mcbond_it 0.525 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1928 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing