2PRV

Crystal structure of an uncharacterized protein (yobk, bsu18990) from bacillus subtilis at 1.30 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6293NANODROP, 2.5M Ammonium sulfate, 0.15M Potassium sodium tartrate, 0.1M Citric acid pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1642.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.128α = 84.54
b = 45.2β = 67.52
c = 48.083γ = 73.12
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2007-04-06MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837, 0.97928, 0.97895SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.324.26894.50.0550.0557.23.969476
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.31.3392.30.5240.5241.43.95045

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)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 DIFFRACTIONMADTHROUGHOUT1.324.26869476349894.540.1370.1370.1350.175RANDOM14.001
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]
-1.850.930.82-0.65-0.211.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.173
r_dihedral_angle_4_deg25.872
r_dihedral_angle_3_deg13.309
r_sphericity_free7.676
r_scangle_it7.009
r_dihedral_angle_1_deg6.444
r_scbond_it5.472
r_sphericity_bonded5.316
r_mcangle_it3.993
r_mcbond_it3.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.173
r_dihedral_angle_4_deg25.872
r_dihedral_angle_3_deg13.309
r_sphericity_free7.676
r_scangle_it7.009
r_dihedral_angle_1_deg6.444
r_scbond_it5.472
r_sphericity_bonded5.316
r_mcangle_it3.993
r_mcbond_it3.222
r_rigid_bond_restr2.503
r_mcbond_other2.137
r_angle_refined_deg1.66
r_angle_other_deg1.111
r_symmetry_vdw_other0.272
r_symmetry_vdw_refined0.229
r_nbd_refined0.221
r_nbtor_refined0.194
r_nbd_other0.192
r_chiral_restr0.189
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.155
r_nbtor_other0.092
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2483
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms70

Software

Software
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
autoSHARPphasing