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2.4 Angstrom crystal structure of fumarate hydratase from Rickettsia prowazekii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3E04
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 289 1.4 M Na Malonate, 39.5 mg/ml, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.02 59.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.9 α = 90 b = 144.9 β = 90 c = 106.21 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 315 2008-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 2.4 19.74 97.5 0.12 9.49 49359 -3
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 2.4 2.46 99.7 0.73 2.7
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 3E04 2.4 19.74 46831 2502 97.75 0.19437 0.19267 0.1991 0.22608 0.2285 RANDOM 20.275
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] -0.5 -0.25 -0.5 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.999 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 14.445 r_dihedral_angle_1_deg 5.072 r_scangle_it 1.698 r_angle_refined_deg 1.043 r_scbond_it 0.997 r_angle_other_deg 0.857 r_mcangle_it 0.632 r_mcbond_it 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.999 r_dihedral_angle_4_deg 19.006 r_dihedral_angle_3_deg 14.445 r_dihedral_angle_1_deg 5.072 r_scangle_it 1.698 r_angle_refined_deg 1.043 r_scbond_it 0.997 r_angle_other_deg 0.857 r_mcangle_it 0.632 r_mcbond_it 0.331 r_mcbond_other 0.068 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 6571 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 15
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling