2ZWM

Crystal structure of YycF receiver domain from Bacillus subtilis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.2M Potassium sodium tartrate tetrahydrate, 0.1M tri-Sodium citrate dihydrate, 2.0M Ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5952.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.824α = 90
b = 58.824β = 90
c = 78.247γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402007-03-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
12.0425.4799.60.06215.65.61921819194337
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)
2.042.151000.4173.75.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2A9R2.0425.47191901919093599.60.19480.195430.193620.22982RANDOM50.533
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]
1.330.661.33-1.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.043
r_dihedral_angle_4_deg19.67
r_dihedral_angle_3_deg15.651
r_dihedral_angle_1_deg6.71
r_scangle_it6.313
r_mcangle_it4.38
r_scbond_it3.813
r_mcbond_it2.482
r_angle_refined_deg1.886
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.043
r_dihedral_angle_4_deg19.67
r_dihedral_angle_3_deg15.651
r_dihedral_angle_1_deg6.71
r_scangle_it6.313
r_mcangle_it4.38
r_scbond_it3.813
r_mcbond_it2.482
r_angle_refined_deg1.886
r_nbtor_refined0.311
r_symmetry_vdw_refined0.254
r_nbd_refined0.225
r_xyhbond_nbd_refined0.142
r_chiral_restr0.128
r_symmetry_hbond_refined0.071
r_bond_refined_d0.02
r_gen_planes_refined0.006
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_refined
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 AtomsNumber
Protein Atoms1922
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing