2Q7F

Crystal structure of YrrB: a TPR protein with an unusual peptide-binding site


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.829440MM PHOTASSIUM PHOSPHATE(KH2PO4), 4% PEG 6000, 20% GLYCEROL, PH 4.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 4.80
Crystal Properties
Matthew coefficientSolvent content
2.140.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.938α = 90
b = 85.139β = 130.63
c = 69.048γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4APAL/PLS4A

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
12.493095.10.0913.914817-3
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)
12.492.5976.70.2432.62.51183

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.4928.4813328148894.90.2110.2060.256RANDOM59.84
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]
0.520.05-0.520.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.268
r_dihedral_angle_4_deg20.48
r_dihedral_angle_3_deg18.991
r_dihedral_angle_1_deg4.844
r_scangle_it1.776
r_scbond_it1.043
r_mcangle_it0.802
r_mcbond_it0.435
r_nbtor_refined0.303
r_nbd_refined0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.268
r_dihedral_angle_4_deg20.48
r_dihedral_angle_3_deg18.991
r_dihedral_angle_1_deg4.844
r_scangle_it1.776
r_scbond_it1.043
r_mcangle_it0.802
r_mcbond_it0.435
r_nbtor_refined0.303
r_nbd_refined0.215
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.097
r_chiral_restr0.074
r_gen_planes_refined0.003
r_xyhbond_nbd_other
r_bond_other_d
r_metal_ion_refined
r_metal_ion_other
r_gen_planes_other
r_symmetry_vdw_other
r_bond_refined_d
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_other
r_mcbond_other
r_angle_refined_deg
r_nbtor_other
r_angle_other_deg
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3048
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms

Software

Software
Software NamePurpose
SOLVEphasing
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling