2QSV

Crystal structure of protein of unknown function from Porphyromonas gingivalis W83


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5298Saturated sucrose, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
4.1870.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.237α = 90
b = 107.237β = 90
c = 59.833γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray150CCDSBC-22007-06-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97945APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.192.8594.623401221392
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1848.4

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 DIFFRACTIONSADTHROUGHOUT2.146.422213922139119699.710.205260.203820.23285RANDOM38.671
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]
0.950.480.95-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.581
r_dihedral_angle_4_deg17.569
r_dihedral_angle_3_deg17.469
r_dihedral_angle_1_deg7.645
r_scangle_it4.749
r_scbond_it2.827
r_mcangle_it1.981
r_angle_refined_deg1.658
r_mcbond_it1.087
r_metal_ion_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.581
r_dihedral_angle_4_deg17.569
r_dihedral_angle_3_deg17.469
r_dihedral_angle_1_deg7.645
r_scangle_it4.749
r_scbond_it2.827
r_mcangle_it1.981
r_angle_refined_deg1.658
r_mcbond_it1.087
r_metal_ion_refined0.322
r_nbtor_refined0.304
r_symmetry_vdw_refined0.259
r_nbd_refined0.238
r_xyhbond_nbd_refined0.182
r_symmetry_hbond_refined0.166
r_chiral_restr0.108
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_metal_ion_other
r_nbd_other
r_symmetry_vdw_other
r_angle_other_deg
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbtor_other
r_mcbond_other
r_gen_planes_other
r_bond_other_d
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1661
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHARPphasing