2F7F

Crystal structure of Enterococcus faecalis putative nicotinate phosphoribosyltransferase, NEW YORK STRUCTURAL GENOMICS CONSORTIUM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1YTD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290100 mM HEPES, 2 M AMMONIUM SULFATE, 10% GLYCEROL, PH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.4749.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.325α = 90
b = 110.627β = 90
c = 154.189γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2005-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
125099.80.1010.0667.37417204157714.6
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)
122.0799.20.630.662.26.44095

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1YTD2204126440207130899.910.22130.172030.170660.21362RANDOM27.365
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]
0.071.63-1.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.703
r_dihedral_angle_4_deg24.085
r_dihedral_angle_3_deg14.936
r_dihedral_angle_1_deg8.12
r_scangle_it1.868
r_mcangle_it1.763
r_angle_refined_deg1.365
r_scbond_it1.207
r_mcbond_it1.164
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.703
r_dihedral_angle_4_deg24.085
r_dihedral_angle_3_deg14.936
r_dihedral_angle_1_deg8.12
r_scangle_it1.868
r_mcangle_it1.763
r_angle_refined_deg1.365
r_scbond_it1.207
r_mcbond_it1.164
r_nbtor_refined0.309
r_chiral_restr0.226
r_symmetry_hbond_refined0.223
r_xyhbond_nbd_refined0.202
r_nbd_refined0.185
r_symmetry_vdw_refined0.158
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3884
Nucleic Acid Atoms
Solvent Atoms390
Heterogen Atoms73

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement