4MZY

Crystal structure of enterococcus faecalis nicotinate phosphoribosyltransferase with malonate and phosphate bound


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2F7FPDB entry 2F7F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72902.4 M SODIUM MALONATE, 10% GLYCEROL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.4649.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.254α = 90
b = 111.381β = 90
c = 154.604γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2007-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

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
11.955099.80.0740.0747.94.144766-5
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)
11.951.981000.6690.6691.94

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 REPLACEMENTTHROUGHOUTPDB entry 2F7F1.9525.7843356139699.560.154770.15370.18587RANDOM35.95
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]
-0.622.71-2.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_4_deg20.321
r_dihedral_angle_3_deg14.008
r_dihedral_angle_1_deg5.708
r_angle_refined_deg1.317
r_angle_other_deg0.754
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.778
r_dihedral_angle_4_deg20.321
r_dihedral_angle_3_deg14.008
r_dihedral_angle_1_deg5.708
r_angle_refined_deg1.317
r_angle_other_deg0.754
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3913
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms110

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling