3QNA

Crystal structure of a 6-pyruvoyltetrahydropterin synthase homologue from Esherichia coli complexed sepiapterin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3QN9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72910.16M tri-ammonium citrate pH 7.0, 16% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.6553.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.714α = 90
b = 115.882β = 90
c = 155.185γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102009-05-22MSINGLE WAVELENGTH
21CCDADSC QUANTUM 2102007-10-24
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C11.000PAL/PLS6C1
2SYNCHROTRONPAL/PLS BEAMLINE 6B1.1123PAL/PLS6B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.49692.85199.90.06914.3355853558522
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.49692.85199.90.0697.335585

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 REPLACEMENTTHROUGHOUT3QN92.592.853558535585338050.183990.18160.23029RANDOM25.15
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]
-1.041.25-0.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.023
r_dihedral_angle_3_deg17.42
r_dihedral_angle_4_deg15.205
r_dihedral_angle_1_deg6.852
r_scangle_it4.759
r_scbond_it3.076
r_angle_refined_deg1.922
r_mcangle_it1.896
r_mcbond_it0.959
r_chiral_restr0.134
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.023
r_dihedral_angle_3_deg17.42
r_dihedral_angle_4_deg15.205
r_dihedral_angle_1_deg6.852
r_scangle_it4.759
r_scbond_it3.076
r_angle_refined_deg1.922
r_mcangle_it1.896
r_mcbond_it0.959
r_chiral_restr0.134
r_bond_refined_d0.022
r_gen_planes_refined0.01
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5658
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms108

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling