2P4Z

A Ferredoxin-like Metallo-beta-lactamase Superfamily Protein from Thermoanaerobacter tengcongensis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529324.5% Pentaerythritol propoxylate (5/4 PO/OH), 0.1M Bis-Tris, 0.08M Ammonium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.197α = 90
b = 138.31β = 90
c = 52.959γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54178

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
12.1150.078103405634056
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1534056

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT2.11530853165096.170.201180.200230.21855RANDOM25.691
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]
-1.49-1.883.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.685
r_dihedral_angle_4_deg19.389
r_dihedral_angle_3_deg16.553
r_dihedral_angle_1_deg5.771
r_scangle_it2.76
r_scbond_it1.782
r_angle_refined_deg1.278
r_mcangle_it1.121
r_mcbond_it0.895
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.685
r_dihedral_angle_4_deg19.389
r_dihedral_angle_3_deg16.553
r_dihedral_angle_1_deg5.771
r_scangle_it2.76
r_scbond_it1.782
r_angle_refined_deg1.278
r_mcangle_it1.121
r_mcbond_it0.895
r_nbtor_refined0.305
r_nbd_refined0.201
r_symmetry_vdw_refined0.173
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.128
r_chiral_restr0.092
r_bond_refined_d0.01
r_gen_planes_refined0.004
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_refined
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 AtomsNumber
Protein Atoms4374
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing