3X0U

Crystal structure of PirB


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.529820mM Tris, 300mM NaCl, 20% 1,4-butanediol, 0.1M Na-acetate, 15% 2,3-butanediol, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2244.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.897α = 90
b = 128.618β = 90
c = 117.104γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0000NSRRCBL13B1

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
11.75099.70.03424.84.799968996683
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)
11.71.7699.30.5092.54.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.726.2510004794329489199.170.150450.150450.148890.18046RANDOM18.691
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]
0.01-0.10.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.209
r_dihedral_angle_4_deg16.019
r_dihedral_angle_3_deg12.096
r_long_range_B_refined7.093
r_long_range_B_other6.67
r_dihedral_angle_1_deg6.287
r_scangle_other4.465
r_mcangle_it3.106
r_mcangle_other3.105
r_scbond_it2.851
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.209
r_dihedral_angle_4_deg16.019
r_dihedral_angle_3_deg12.096
r_long_range_B_refined7.093
r_long_range_B_other6.67
r_dihedral_angle_1_deg6.287
r_scangle_other4.465
r_mcangle_it3.106
r_mcangle_other3.105
r_scbond_it2.851
r_scbond_other2.85
r_mcbond_it1.943
r_mcbond_other1.942
r_angle_refined_deg1.731
r_angle_other_deg0.87
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6854
Nucleic Acid Atoms
Solvent Atoms995
Heterogen Atoms

Software

Software
Software NamePurpose
Blu-Icedata collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling