6F3O

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa complexed with adenine, K+ and Zn2+ cations


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6F3P 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29250 mM KH2PO4, 20% (w/v) PEG8000, 2 mM 2'-deoxyadenosine
Crystal Properties
Matthews coefficientSolvent content
2.2545.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 170.839α = 90
b = 99.614β = 101.97
c = 111.825γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252014-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.8950BESSY14.3

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
11.752599.90.07817.64.2182928-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.81

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT6F3P1.7525181035180699.690.140030.139760.16712RANDOM25.543
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]
0.03-0.080.24-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.562
r_dihedral_angle_4_deg14.423
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg6.351
r_long_range_B_refined4.235
r_long_range_B_other4.066
r_scangle_other2.501
r_angle_refined_deg1.657
r_scbond_it1.631
r_scbond_other1.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.562
r_dihedral_angle_4_deg14.423
r_dihedral_angle_3_deg12.988
r_dihedral_angle_1_deg6.351
r_long_range_B_refined4.235
r_long_range_B_other4.066
r_scangle_other2.501
r_angle_refined_deg1.657
r_scbond_it1.631
r_scbond_other1.631
r_mcangle_it1.494
r_mcangle_other1.494
r_mcbond_it1.052
r_mcbond_other1.052
r_angle_other_deg0.983
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14196
Nucleic Acid Atoms
Solvent Atoms1616
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
ARP/wARPmodel building