3GP6

Crystal structure of PagP in SDS/MPD


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62911M MPD, 0.1M citrate pH 5.6, 1.7M lithium sulphate, 0.3M ammonium sulphate, SDS, Phase separation, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6553.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.228α = 90
b = 113.228β = 90
c = 55.064γ = 120
Symmetry
Space GroupP 62 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.98APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.42097.70.0688.24043340433-3-321.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.4280.40.5311.364.11633

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENTTHROUGHOUTPDB entry 1THQ1.420-3-33913239132126097.740.172590.172590.171470.20817RANDOM28.065
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]
3.21.63.2-4.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.108
r_dihedral_angle_4_deg18.014
r_sphericity_free15.265
r_dihedral_angle_3_deg13.991
r_sphericity_bonded9.638
r_dihedral_angle_1_deg7.084
r_scangle_it5.134
r_scbond_it4.125
r_mcangle_it3.806
r_mcbond_it2.793
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.108
r_dihedral_angle_4_deg18.014
r_sphericity_free15.265
r_dihedral_angle_3_deg13.991
r_sphericity_bonded9.638
r_dihedral_angle_1_deg7.084
r_scangle_it5.134
r_scbond_it4.125
r_mcangle_it3.806
r_mcbond_it2.793
r_rigid_bond_restr2.612
r_angle_refined_deg2.119
r_mcbond_other1.726
r_angle_other_deg0.96
r_xyhbond_nbd_refined0.244
r_symmetry_vdw_other0.242
r_nbd_refined0.236
r_symmetry_hbond_refined0.222
r_metal_ion_refined0.217
r_nbtor_refined0.199
r_nbd_other0.193
r_symmetry_vdw_refined0.183
r_chiral_restr0.137
r_symmetry_metal_ion_refined0.105
r_nbtor_other0.092
r_xyhbond_nbd_other0.042
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.002
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1258
Nucleic Acid Atoms
Solvent Atoms56
Heterogen Atoms209

Software

Software
Software NamePurpose
HKL-3000data collection
EPMRphasing
REFMACrefinement
HKL-3000data reduction
SCALEPACKdata scaling