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Structure of a monoclinic crystal form of human cytosolic aconitase (IRP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.1 293 pH 8.1, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.91 α = 90 b = 215.47 β = 72 c = 64.01 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2003-04-05 M SINGLE WAVELENGTH 2 1 x-ray 2003-09-04 M SINGLE WAVELENGTH 2,1 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4 2 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 2,1 1.85 29.5 99 0.063 8.6 2 138110
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) 2,1 1.85 2 92.1 0.262 3 1.8
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 2B3X 1.85 29.5 131161 6949 94 0.213 0.211 0.2141 0.261 0.264 RANDOM 27.94
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] -0.96 0.2 2.36 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 15.811 r_dihedral_angle_1_deg 5.89 r_scangle_it 4.108 r_scbond_it 3.168 r_mcangle_it 1.986 r_mcbond_it 1.485 r_angle_refined_deg 1.293 r_metal_ion_refined 0.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.225 r_dihedral_angle_3_deg 16.068 r_dihedral_angle_4_deg 15.811 r_dihedral_angle_1_deg 5.89 r_scangle_it 4.108 r_scbond_it 3.168 r_mcangle_it 1.986 r_mcbond_it 1.485 r_angle_refined_deg 1.293 r_metal_ion_refined 0.337 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.225 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.198 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other 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 13856 Nucleic Acid Atoms Solvent Atoms 970 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing