2V4N

Crystal structure of Salmonella typhimurium SurE at 1.7 angstrom resolution in orthorhombic form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J9JPDB ENTRY 1J9J

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.50.2M TRISODIUM CITRATE DIHYDRATE, 0.1M HEPES PH 7.5, 30% MPD MICROBATCH METHOD
Crystal Properties
Matthews coefficientSolvent content
2.7755.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.73α = 90
b = 121.638β = 90
c = 143.256γ = 90
Symmetry
Space GroupF 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.75099.70.0426.35.635384
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)
11.75097.80.482.334.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1J9J1.771.6133610177399.590.184460.182970.21227RANDOM25.555
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]
0.99-0.9-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.126
r_dihedral_angle_4_deg16.178
r_dihedral_angle_3_deg11.677
r_dihedral_angle_1_deg5.708
r_scangle_it2.081
r_scbond_it1.366
r_angle_refined_deg1.072
r_mcangle_it0.824
r_mcbond_it0.484
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.126
r_dihedral_angle_4_deg16.178
r_dihedral_angle_3_deg11.677
r_dihedral_angle_1_deg5.708
r_scangle_it2.081
r_scbond_it1.366
r_angle_refined_deg1.072
r_mcangle_it0.824
r_mcbond_it0.484
r_nbtor_refined0.299
r_nbd_refined0.192
r_symmetry_vdw_refined0.161
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.121
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.003
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1896
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing