4FGR

X-Ray Structure of SAICAR Synthetase (PurC) from Streptococcus pneumoniae complexed with ADP and Mg2+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GQRPDB ENTRY 2GQR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828936% PEG 200, 0.16 M Sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.243.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.931α = 90
b = 65.111β = 91.96
c = 85.837γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102011-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-BM

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
12.59785.78784.80.0920.09211.922.7123231190211
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5972.66458.66

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2GQR2.59785.75123231232364682.090.234980.23060.31866RANDOM43.9
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]
5.244.68-3.99-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.876
r_dihedral_angle_3_deg23.302
r_dihedral_angle_4_deg17.555
r_dihedral_angle_1_deg7.665
r_angle_refined_deg1.637
r_chiral_restr0.11
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.876
r_dihedral_angle_3_deg23.302
r_dihedral_angle_4_deg17.555
r_dihedral_angle_1_deg7.665
r_angle_refined_deg1.637
r_chiral_restr0.11
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3799
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms65

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling