3KCQ

Crystal structure of phosphoribosylglycinamide formyltransferase from anaplasma phagocytophilum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5EMERALD JCSG SCREEN CONDITION A2. 100 MM CITRATE PH 5.0, 20% PEG 3000. PROTEIN CONCENTRATION 54 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.8757.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.45α = 90
b = 125.247β = 95.44
c = 138.537γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252009-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97953CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.25085.40.0819.73.445778
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)
12.22.2481.90.4493.3

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 REPLACEMENTTHROUGHOUT1ZLY2.2504577723240.2120.210.263RANDOM14.24
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]
-1.650.29-1.353.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.084
r_dihedral_angle_3_deg16.716
r_dihedral_angle_4_deg16.149
r_dihedral_angle_1_deg5.915
r_scangle_it2.844
r_scbond_it1.758
r_angle_refined_deg1.366
r_mcangle_it1.154
r_angle_other_deg0.901
r_mcbond_it0.623
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.084
r_dihedral_angle_3_deg16.716
r_dihedral_angle_4_deg16.149
r_dihedral_angle_1_deg5.915
r_scangle_it2.844
r_scbond_it1.758
r_angle_refined_deg1.366
r_mcangle_it1.154
r_angle_other_deg0.901
r_mcbond_it0.623
r_mcbond_other0.134
r_chiral_restr0.079
r_bond_refined_d0.013
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6231
Nucleic Acid Atoms
Solvent Atoms205
Heterogen Atoms24

Software

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