2Z2O | pdb_00002z2o

Crystal Structure of apo virginiamycin B lyase from Staphylococcus aureus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z2NPDB entry 2Z2N

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529550mM acetate buffer (pH 4.6), 25%(w/v) PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.0740.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.543α = 90
b = 79.231β = 90
c = 188.168γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 42005-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X8C1.0999NSLSX8C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.95098.90.08119.44.586401
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.9793.90.4613.53.1

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2Z2N1.919.8978962810899.740.146030.140290.150.199020.21RANDOM21.662
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.371
r_dihedral_angle_4_deg19.3
r_dihedral_angle_3_deg15.234
r_dihedral_angle_1_deg6.498
r_scangle_it4.29
r_scbond_it2.961
r_angle_refined_deg1.843
r_mcangle_it1.841
r_mcbond_it1.227
r_angle_other_deg0.963
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.371
r_dihedral_angle_4_deg19.3
r_dihedral_angle_3_deg15.234
r_dihedral_angle_1_deg6.498
r_scangle_it4.29
r_scbond_it2.961
r_angle_refined_deg1.843
r_mcangle_it1.841
r_mcbond_it1.227
r_angle_other_deg0.963
r_mcbond_other0.358
r_symmetry_vdw_refined0.247
r_symmetry_vdw_other0.245
r_symmetry_hbond_refined0.242
r_nbd_refined0.215
r_xyhbond_nbd_refined0.205
r_nbd_other0.199
r_nbtor_refined0.176
r_chiral_restr0.13
r_nbtor_other0.087
r_bond_refined_d0.022
r_gen_planes_refined0.008
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 Atoms9210
Nucleic Acid Atoms
Solvent Atoms1083
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing