1VPH

CRYSTAL STRUCTURE OF a YbjQ-like protein of unknown function (SSO2532) FROM SULFOLOBUS SOLFATARICUS P2 AT 1.76 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION,SITTING DROP,NANODROP7.527710.0% iso-Propanol, 20.0% PEG-4000, 0.1M HEPES pH7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.1341.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.86α = 90
b = 92.18β = 90
c = 114.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152004-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
11.76428.6890.90.06215.63.97589731.06
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)
11.7641.8663.60.31231.97634

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1VMF1.76416.2272013379190.690.190820.189140.22173RANDOM22.167
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]
0.58-2.011.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.54
r_dihedral_angle_3_deg14.27
r_dihedral_angle_4_deg11.353
r_scangle_it6.712
r_dihedral_angle_1_deg6.46
r_scbond_it4.767
r_mcangle_it2.714
r_angle_refined_deg1.607
r_mcbond_it1.599
r_angle_other_deg0.961
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.54
r_dihedral_angle_3_deg14.27
r_dihedral_angle_4_deg11.353
r_scangle_it6.712
r_dihedral_angle_1_deg6.46
r_scbond_it4.767
r_mcangle_it2.714
r_angle_refined_deg1.607
r_mcbond_it1.599
r_angle_other_deg0.961
r_metal_ion_refined0.479
r_mcbond_other0.371
r_nbd_refined0.272
r_symmetry_vdw_other0.267
r_nbd_other0.202
r_nbtor_refined0.182
r_symmetry_vdw_refined0.165
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.148
r_xyhbond_nbd_other0.128
r_chiral_restr0.1
r_nbtor_other0.09
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6658
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms64

Software

Software
Software NamePurpose
SOLVEphasing
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4data scaling