3KKW

Crystal structure of His-tagged form of PA4794 protein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I6C 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52931.5 M Ammonium Sulfate, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.534α = 90
b = 76.145β = 90
c = 39.454γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rmirrors2009-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9792APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.415099.90.0470.04747.196.53417434174-314.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.411.431000.3910.3914.185.71658

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2i6c1.4145.93239832398172799.890.157490.157490.156280.17922RANDOM13.124
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]
0.26-0.280.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.085
r_dihedral_angle_4_deg14.234
r_dihedral_angle_3_deg11.405
r_dihedral_angle_1_deg5.743
r_scangle_it4.428
r_angle_other_deg4.103
r_scbond_it2.877
r_mcangle_it1.974
r_angle_refined_deg1.818
r_mcbond_it1.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.085
r_dihedral_angle_4_deg14.234
r_dihedral_angle_3_deg11.405
r_dihedral_angle_1_deg5.743
r_scangle_it4.428
r_angle_other_deg4.103
r_scbond_it2.877
r_mcangle_it1.974
r_angle_refined_deg1.818
r_mcbond_it1.169
r_chiral_restr0.112
r_bond_refined_d0.019
r_gen_planes_other0.014
r_gen_planes_refined0.01
r_bond_other_d
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1326
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms78

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-3000phasing
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling