4EWT

The crystal structure of a putative aminohydrolase from methicillin resistant Staphylococcus aureus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YSJPDB ENTRY 1YSJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52980.2M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.5, 30.0% PEG 400, Microbatch under oil, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.6566.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.62α = 115.4
b = 120.11β = 94.64
c = 132.41γ = 96.55
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDMIRRORS2011-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9762ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.140.0993.80.1110.0677.53.5133741226.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2188.60.4040.2532.93.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1YSJ2.139.32127008673193.80.20.1990.229RANDOM38.361
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]
-0.191.380.741.951.880.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.907
r_dihedral_angle_3_deg16.687
r_dihedral_angle_4_deg15.905
r_dihedral_angle_1_deg5.752
r_scangle_it2.699
r_scbond_it1.606
r_angle_refined_deg1.205
r_mcangle_it0.88
r_mcbond_it0.454
r_chiral_restr0.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.907
r_dihedral_angle_3_deg16.687
r_dihedral_angle_4_deg15.905
r_dihedral_angle_1_deg5.752
r_scangle_it2.699
r_scbond_it1.606
r_angle_refined_deg1.205
r_mcangle_it0.88
r_mcbond_it0.454
r_chiral_restr0.086
r_bond_refined_d0.01
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11751
Nucleic Acid Atoms
Solvent Atoms475
Heterogen Atoms81

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling