☰ Navigation Tabs
Crystal Structure of catalytically inactive H270A virginiamycin B lyase from Staphylococcus aureus with Quinupristin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z2N PDB ENTRY 2Z2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100MM 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 coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.999 α = 90 b = 93.7 β = 90 c = 95.301 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 IMAGE PLATE RIGAKU RAXIS IV++ 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 50 91.1 0.136 6 4.1 14813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.99 94.1 0.31 3.8 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2Z2N 2.8 36.18 13189 1587 91.2 0.268 0.262 0.2719 0.318 0.318 RANDOM 20.33
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.518 r_dihedral_angle_3_deg 18.149 r_dihedral_angle_4_deg 11.864 r_dihedral_angle_1_deg 8.874 r_angle_refined_deg 1.512 r_scangle_it 0.972 r_mcangle_it 0.752 r_mcbond_it 0.548 r_scbond_it 0.541 r_chiral_restr 0.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.518 r_dihedral_angle_3_deg 18.149 r_dihedral_angle_4_deg 11.864 r_dihedral_angle_1_deg 8.874 r_angle_refined_deg 1.512 r_scangle_it 0.972 r_mcangle_it 0.752 r_mcbond_it 0.548 r_scbond_it 0.541 r_chiral_restr 0.496 r_symmetry_hbond_refined 0.459 r_symmetry_vdw_refined 0.373 r_nbtor_refined 0.318 r_nbd_refined 0.239 r_xyhbond_nbd_refined 0.181 r_metal_ion_refined 0.152 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 4662 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 120
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling