2Z2P | pdb_00002z2p

Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100MM MES BUFFER (PH 6.5), 20%(W/V) PEG 10000, PROTEIN SOLUTION SUPPLEMENTED WITH 3MM MGCL2, 3MM DALFOPRISTIN, 1MM QUINUPRISTIN, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
Crystal Properties
Matthews coefficientSolvent content
2.448.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.999α = 90
b = 93.7β = 90
c = 95.301γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95IMAGE PLATERIGAKU RAXIS IV++2006-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
12.85091.10.13664.114813
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)
12.82.9994.10.313.83.8

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 2Z2N2.836.1813189158791.20.2680.2620.270.3180.32RANDOM20.33
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.518
r_dihedral_angle_3_deg18.149
r_dihedral_angle_4_deg11.864
r_dihedral_angle_1_deg8.874
r_angle_refined_deg1.512
r_scangle_it0.972
r_mcangle_it0.752
r_mcbond_it0.548
r_scbond_it0.541
r_chiral_restr0.496
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.518
r_dihedral_angle_3_deg18.149
r_dihedral_angle_4_deg11.864
r_dihedral_angle_1_deg8.874
r_angle_refined_deg1.512
r_scangle_it0.972
r_mcangle_it0.752
r_mcbond_it0.548
r_scbond_it0.541
r_chiral_restr0.496
r_symmetry_hbond_refined0.459
r_symmetry_vdw_refined0.373
r_nbtor_refined0.318
r_nbd_refined0.239
r_xyhbond_nbd_refined0.181
r_metal_ion_refined0.152
r_bond_refined_d0.009
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_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 Atoms4662
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms120

Software

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