3E3X

The C-terminal part of BipA protein from Vibrio parahaemolyticus RIMD 2210633


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.52770.1 M Hepes, 20 % PEG 4k 10% Isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3547.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.6α = 90
b = 104.571β = 90
c = 74.348γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDADSC QUANTUM 315MIRRORS2008-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-IDAPS19-ID

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
11.954099.80.0929.87.3258712
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)
11.951.981000.5647.2

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.95402583824524131499.60.1740.1720.223RANDOM17.25
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]
0.62-0.850.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.381
r_dihedral_angle_4_deg15.382
r_dihedral_angle_3_deg14.358
r_dihedral_angle_1_deg6.465
r_scangle_it4.618
r_scbond_it3.065
r_angle_refined_deg1.845
r_mcangle_it1.597
r_mcbond_it1.39
r_angle_other_deg0.989
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.381
r_dihedral_angle_4_deg15.382
r_dihedral_angle_3_deg14.358
r_dihedral_angle_1_deg6.465
r_scangle_it4.618
r_scbond_it3.065
r_angle_refined_deg1.845
r_mcangle_it1.597
r_mcbond_it1.39
r_angle_other_deg0.989
r_symmetry_hbond_refined0.55
r_mcbond_other0.312
r_symmetry_vdw_other0.306
r_nbd_other0.216
r_nbd_refined0.214
r_xyhbond_nbd_refined0.182
r_nbtor_refined0.177
r_symmetry_vdw_refined0.175
r_chiral_restr0.099
r_nbtor_other0.091
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2261
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXphasing
ARPmodel building
Cootmodel building
MLPHAREphasing
CCP4phasing