2B0P

truncated S. aureus LytM, P212121 crystal form


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.82940.2 M ammonium sulfate, 0.1 M sodium cacodylate, 0.1 M sodium acetate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.346

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.093α = 90
b = 78.261β = 90
c = 102.049γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-11-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMPG/DESY, HAMBURG BEAMLINE BW61.05MPG/DESY, HAMBURGBW6

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
11.52099.90.0680.0686.43.5421304213013.8
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)
11.51.581000.2560.2562.73.36060

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 REPLACEMENTTHROUGHOUT1QWY1.519.844205939977208299.950.1840.182410.180390.22239RANDOM10.184
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]
2.04-0.46-1.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.232
r_angle_other_deg4.003
r_scangle_it3.884
r_scbond_it2.616
r_angle_refined_deg1.703
r_mcangle_it1.668
r_mcbond_it1.075
r_symmetry_vdw_other0.332
r_nbd_other0.296
r_symmetry_hbond_refined0.212
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.232
r_angle_other_deg4.003
r_scangle_it3.884
r_scbond_it2.616
r_angle_refined_deg1.703
r_mcangle_it1.668
r_mcbond_it1.075
r_symmetry_vdw_other0.332
r_nbd_other0.296
r_symmetry_hbond_refined0.212
r_nbd_refined0.193
r_xyhbond_nbd_refined0.174
r_chiral_restr0.115
r_nbtor_other0.114
r_metal_ion_refined0.094
r_symmetry_vdw_refined0.082
r_bond_refined_d0.017
r_gen_planes_other0.015
r_gen_planes_refined0.01
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1980
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing