2B13

Truncated S. aureus LytM, P41 crystal form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1QWY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529430 % PEG 8000, 0.2 M L(+)-tartrate, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.3447

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.962α = 90
b = 65.962β = 90
c = 62.96γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOsmic Max-Flux2005-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU300

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
11.5514.896.30.0370.03725.82.2385463854615
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)
11.551.5886.10.1520.152101803

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1QWY1.5514.83660636606194098.20.173030.173030.171570.20054RANDOM12.214
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]
-0.19-0.190.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.79
r_angle_other_deg3.994
r_scangle_it3.779
r_scbond_it2.417
r_mcangle_it1.511
r_angle_refined_deg1.48
r_mcbond_it0.87
r_nbd_other0.298
r_symmetry_vdw_other0.289
r_nbd_refined0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.79
r_angle_other_deg3.994
r_scangle_it3.779
r_scbond_it2.417
r_mcangle_it1.511
r_angle_refined_deg1.48
r_mcbond_it0.87
r_nbd_other0.298
r_symmetry_vdw_other0.289
r_nbd_refined0.222
r_xyhbond_nbd_refined0.141
r_symmetry_hbond_refined0.136
r_nbtor_other0.115
r_symmetry_vdw_refined0.107
r_chiral_restr0.096
r_metal_ion_refined0.036
r_bond_refined_d0.013
r_gen_planes_other0.009
r_gen_planes_refined0.007
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms2004
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing