2GUK

Crystal Structure of the Conserved Protein of Unknown Function from Porphyromonas gingivalis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52755% iso-propanol, 0.1 M HEPES 7.5, 10 % PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 275K
Crystal Properties
Matthews coefficientSolvent content
2.0640.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.028α = 90
b = 50.028β = 90
c = 186.912γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2006-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97933APS19-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
11.9134.7698.60.11510.520.72013819279
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)
11.911.9896.70.822.211.41825

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 DIFFRACTIONSADTHROUGHOUT1.9134.761716817168195398.640.237420.237420.232530.28056RANDOM31.333
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]
0.770.77-1.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.093
r_dihedral_angle_4_deg20.883
r_dihedral_angle_3_deg19.238
r_dihedral_angle_1_deg5.407
r_scangle_it3.332
r_scbond_it2.219
r_angle_refined_deg1.487
r_mcangle_it1.484
r_mcbond_it0.957
r_nbd_refined0.239
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.093
r_dihedral_angle_4_deg20.883
r_dihedral_angle_3_deg19.238
r_dihedral_angle_1_deg5.407
r_scangle_it3.332
r_scbond_it2.219
r_angle_refined_deg1.487
r_mcangle_it1.484
r_mcbond_it0.957
r_nbd_refined0.239
r_symmetry_vdw_refined0.208
r_symmetry_hbond_refined0.207
r_xyhbond_nbd_refined0.176
r_chiral_restr0.127
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms1826
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
RESOLVEphasing
SHELXEmodel building
SHELXDphasing