3BDD

CRYSTAL STRUCTURE OF A PUTATIVE MULTIPLE ANTIBIOTIC-RESISTANCE REPRESSOR (SSU05_1136) FROM STREPTOCOCCUS SUIS 89/1591 AT 2.20 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.2277NANODROP, 0.2M NaCl, 20.0% PEG 8000, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4750.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.734α = 90
b = 100.43β = 111.42
c = 68.695γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-08-30MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0000, 0.9798ALS8.2.2

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
12.215.89595.60.0660.0667.91.93106837.26
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)
12.22.3297.10.4170.4171.71.94574

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.215.89531066158195.450.2250.2230.275RANDOM39.499
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]
0.510.16-0.35-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.684
r_dihedral_angle_3_deg10.745
r_dihedral_angle_4_deg10.545
r_scangle_it4.372
r_dihedral_angle_1_deg3.131
r_scbond_it3.07
r_angle_refined_deg1.411
r_mcangle_it1.288
r_angle_other_deg1.275
r_mcbond_it0.977
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.684
r_dihedral_angle_3_deg10.745
r_dihedral_angle_4_deg10.545
r_scangle_it4.372
r_dihedral_angle_1_deg3.131
r_scbond_it3.07
r_angle_refined_deg1.411
r_mcangle_it1.288
r_angle_other_deg1.275
r_mcbond_it0.977
r_mcbond_other0.199
r_nbd_refined0.15
r_nbtor_refined0.133
r_symmetry_vdw_other0.13
r_nbd_other0.111
r_xyhbond_nbd_refined0.084
r_chiral_restr0.081
r_nbtor_other0.071
r_symmetry_hbond_refined0.057
r_symmetry_vdw_refined0.055
r_bond_refined_d0.012
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4333
Nucleic Acid Atoms
Solvent Atoms224
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SHELXDphasing
SHARPphasing