3P85

Crystal structure enoyl-coa hydratase from mycobacterium avium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H81PDB entry 3h81 modified with CCP4 program CHAINSAW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5290EBS JCSG+ SCREEN D10: 100MM CACODYLATE PH 6.5, 200MM CAOAC2, 40% PEG 400; MYAVA.01556.A.A1 PS00705 AT 75MG/ML, PH N/A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.9758.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.29α = 90
b = 127.29β = 90
c = 72.9γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+RIGAKU VariMax HF2010-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.950990.08523.95162795427674-326.19
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9599.90.4964.48.32019

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3h81 modified with CCP4 program CHAINSAW1.947.942795427548138098.60.1850.1850.1830.216RANDOM17.63
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]
-1.94-0.97-1.942.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.531
r_dihedral_angle_4_deg19.382
r_dihedral_angle_3_deg12.446
r_dihedral_angle_1_deg6.076
r_scangle_it3.734
r_scbond_it2.28
r_angle_other_deg1.572
r_angle_refined_deg1.476
r_mcangle_it1.302
r_mcbond_it0.723
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.531
r_dihedral_angle_4_deg19.382
r_dihedral_angle_3_deg12.446
r_dihedral_angle_1_deg6.076
r_scangle_it3.734
r_scbond_it2.28
r_angle_other_deg1.572
r_angle_refined_deg1.476
r_mcangle_it1.302
r_mcbond_it0.723
r_mcbond_other0.125
r_chiral_restr0.099
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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 AtomsNumber
Protein Atoms1645
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms28

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling