4FE2

X-Ray Structure of SAICAR Synthetase (PurC) from Streptococcus pneumoniae complexed with AIR, ADP, Asp 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 DROP828940% PEG 200, 0.16 Sodium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2144.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.074α = 90
b = 65.021β = 92.09
c = 86.052γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCD2011-11-04MSINGLE 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
12.28885.99599.50.0810.08125.93.7229852160111
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.2882.399.40.197.9

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 2GQR2.28885.992298521601116498.510.200780.196410.28431RANDOM27.709
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]
2.852.44-2.58-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.416
r_dihedral_angle_3_deg19.484
r_dihedral_angle_4_deg17.111
r_dihedral_angle_1_deg7.35
r_angle_refined_deg2.023
r_chiral_restr0.122
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.416
r_dihedral_angle_3_deg19.484
r_dihedral_angle_4_deg17.111
r_dihedral_angle_1_deg7.35
r_angle_refined_deg2.023
r_chiral_restr0.122
r_bond_refined_d0.016
r_gen_planes_refined0.008
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 Atoms3802
Nucleic Acid Atoms
Solvent Atoms414
Heterogen Atoms140

Software

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