2YDU

Crystal structure of YopH in complex with 3-(1,1-dioxido-3- oxoisothiazolidin-5-yl)benzaldeyde


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5MORPHEUS E8 (0.1M BUFFER SYSTEM 2 PH 7.5, 0.12 M ETHYLENE GLYCOLS, 12.5% V/V MPD, 12.5% W/V PEG 3350, , 12.5% W/V PEG 1000)
Crystal Properties
Matthews coefficientSolvent content
2.0339.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.307α = 90
b = 55.912β = 90
c = 99.055γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100MARRESEARCHVARIMAX HR-HF2010-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
11.785095.70.0535.56.4258452
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)
11.781.8463.40.412.63.4

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 1QZ01.7949.5124486130296.60.177780.175890.21323RANDOM18.758
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]
-1.030.050.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.156
r_dihedral_angle_4_deg15.204
r_dihedral_angle_3_deg11.912
r_dihedral_angle_1_deg6.096
r_scangle_it4.399
r_scbond_it2.759
r_mcangle_it1.656
r_angle_refined_deg1.572
r_angle_other_deg0.916
r_mcbond_it0.872
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.156
r_dihedral_angle_4_deg15.204
r_dihedral_angle_3_deg11.912
r_dihedral_angle_1_deg6.096
r_scangle_it4.399
r_scbond_it2.759
r_mcangle_it1.656
r_angle_refined_deg1.572
r_angle_other_deg0.916
r_mcbond_it0.872
r_mcbond_other0.22
r_chiral_restr0.102
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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_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 Atoms2166
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing