5A0F | pdb_00005a0f

Crystal structure of Yersinia Afp18-modified RhoA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DPFPDB ENTRY 1DPF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.150.1 M SODIUM ACETATE, PH 5 AND 1.5 M AMMONIUM SULFATE; SITTING-DROP VAPOR-DIFFUSION AT 293.15 K
Crystal Properties
Matthews coefficientSolvent content
2.9358.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.392α = 90
b = 91.392β = 90
c = 56.628γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCD2014-02-21MSINGLE 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
12501000.1121.35.8319412
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)
122.071000.325.55.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1DPF291.391593786699.770.205710.205330.220.212920.23RANDOM19.808
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]
-0.51-0.511.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.105
r_dihedral_angle_4_deg21.436
r_dihedral_angle_3_deg12.846
r_dihedral_angle_1_deg5.258
r_angle_other_deg2.366
r_scbond_it2.109
r_mcangle_it1.901
r_angle_refined_deg1.671
r_mcbond_it1.237
r_mcbond_other1.236
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.105
r_dihedral_angle_4_deg21.436
r_dihedral_angle_3_deg12.846
r_dihedral_angle_1_deg5.258
r_angle_other_deg2.366
r_scbond_it2.109
r_mcangle_it1.901
r_angle_refined_deg1.671
r_mcbond_it1.237
r_mcbond_other1.236
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_gen_planes_other0.007
r_bond_other_d0.001
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_it
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 Atoms1399
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms47

Software

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