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X-ray crystallographic structure of E. coli apo-EfeB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GVK PDB ENTRY 2GVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 291 2.0M AMMONIUM SULFATE, 5% (V/V) PEG 400, 0.1M HEPES PH 7.0, 291K
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.315 α = 90 b = 86.26 β = 90 c = 119.576 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 CCD 2006-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 60 99.7 0.08 26.5 10.7 58929
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 2.05 98.8 0.24 8 10.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2GVK 2 35 55391 2956 99.02 0.20589 0.20286 0.2026 0.26483 0.2625 RANDOM 29.754
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] -0.09 0.52 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.337 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_4_deg 13.537 r_dihedral_angle_1_deg 6.063 r_scangle_it 3.519 r_scbond_it 2.262 r_mcangle_it 1.56 r_angle_refined_deg 1.42 r_mcbond_it 0.881 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.337 r_dihedral_angle_3_deg 14.957 r_dihedral_angle_4_deg 13.537 r_dihedral_angle_1_deg 6.063 r_scangle_it 3.519 r_scbond_it 2.262 r_mcangle_it 1.56 r_angle_refined_deg 1.42 r_mcbond_it 0.881 r_chiral_restr 0.106 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5832 Nucleic Acid Atoms Solvent Atoms 589 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing