2APL

Crystal structure of protein PG0816 from Porphyromonas gingivalis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298Ammonium Acetate, Bis-Tris, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.651.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.947α = 90
b = 55.159β = 90
c = 80.984γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97954APS19-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
125095.80.06652.46.712416-3
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)
122.0771.90.15711.25.4

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.0145.6123741237460596.860.19870.19870.196920.23367RANDOM38.682
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]
2.35-0.92-1.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.887
r_dihedral_angle_4_deg20.696
r_dihedral_angle_3_deg15.728
r_dihedral_angle_1_deg5.418
r_scangle_it4.609
r_scbond_it3.121
r_mcangle_it1.715
r_angle_refined_deg1.6
r_mcbond_it1.233
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.887
r_dihedral_angle_4_deg20.696
r_dihedral_angle_3_deg15.728
r_dihedral_angle_1_deg5.418
r_scangle_it4.609
r_scbond_it3.121
r_mcangle_it1.715
r_angle_refined_deg1.6
r_mcbond_it1.233
r_nbtor_refined0.302
r_nbd_refined0.216
r_xyhbond_nbd_refined0.153
r_symmetry_vdw_refined0.144
r_chiral_restr0.118
r_symmetry_hbond_refined0.114
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms1192
Nucleic Acid Atoms
Solvent Atoms80
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing