4KJM

Crystal structure of the Staphylococcus aureus protein (NP_646141.1, domain 3912-4037) similar to streptococcal adhesins emb and ebhA/ebhB


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION82772.5M NACL, 0.1M IMIDAZOLE, 0.2M ZN(ACO)2, PH 8.00, VAPOR DIFFUSION, TEMPERATURE 277K
Crystal Properties
Matthews coefficientSolvent content
2.449.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.783α = 90
b = 59.23β = 90
c = 88.186γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-2MIRRORS2004-07-06MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.98011, 0.98031, 0.96487APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
125099.70.05355.02718.31870718652-331
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.071000.26312.716.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT219.28176321753094499.420.187670.187670.185420.22986RANDOM39.356
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]
0.51-0.39-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_dihedral_angle_3_deg14.171
r_dihedral_angle_4_deg8.158
r_dihedral_angle_1_deg4.559
r_angle_refined_deg1.694
r_angle_other_deg1.112
r_chiral_restr0.092
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.343
r_dihedral_angle_3_deg14.171
r_dihedral_angle_4_deg8.158
r_dihedral_angle_1_deg4.559
r_angle_refined_deg1.694
r_angle_other_deg1.112
r_chiral_restr0.092
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.004
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1757
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms28

Software

Software
Software NamePurpose
HKL-2000data collection
SHELXDphasing
MLPHAREphasing
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing