3E04

Crystal structure of human fumarate hydratase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529820% PEG 3350, 10% ethanediol, 0.2 M sodium acetate, 0.1 M bis-tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.7755.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 188.483α = 90
b = 188.483β = 90
c = 114.632γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.952599.30.149.76.216862921
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0696.82523857

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1YFM1.9525166623199599.280.197280.197280.196730.24408RANDOM19.909
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]
-0.51-0.26-0.510.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.248
r_dihedral_angle_4_deg20.659
r_dihedral_angle_3_deg13.361
r_dihedral_angle_1_deg5.715
r_scangle_it2.602
r_scbond_it1.826
r_angle_refined_deg1.419
r_mcangle_it1.052
r_angle_other_deg1.029
r_mcbond_it0.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.248
r_dihedral_angle_4_deg20.659
r_dihedral_angle_3_deg13.361
r_dihedral_angle_1_deg5.715
r_scangle_it2.602
r_scbond_it1.826
r_angle_refined_deg1.419
r_mcangle_it1.052
r_angle_other_deg1.029
r_mcbond_it0.722
r_symmetry_vdw_other0.228
r_nbd_refined0.204
r_mcbond_other0.197
r_nbd_other0.184
r_symmetry_hbond_refined0.175
r_symmetry_vdw_refined0.171
r_nbtor_refined0.168
r_xyhbond_nbd_refined0.14
r_chiral_restr0.085
r_nbtor_other0.085
r_bond_refined_d0.015
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 AtomsNumber
Protein Atoms13145
Nucleic Acid Atoms
Solvent Atoms655
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing