9KQ9 | pdb_00009kq9

The structure of the YcfA-GTP from Erwinia amylovora


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP289.150.2 M sodium malonate pH 7.0 and 20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.957.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.174α = 90
b = 134.366β = 98.35
c = 233.837γ = 90
Symmetry
Space GroupP 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-08-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.979SSRFBL18U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.5947.5199.750.9939.066.8128775
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.5942.6610.608

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.5947.51122219653199.790.213310.210960.21830.257460.2587RANDOM52.65
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]
0.970.24-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.468
r_dihedral_angle_2_deg12.884
r_long_range_B_refined10.328
r_long_range_B_other10.326
r_scangle_other8.811
r_mcangle_other7.277
r_mcangle_it7.276
r_dihedral_angle_1_deg6.424
r_scbond_it6.339
r_scbond_other6.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.468
r_dihedral_angle_2_deg12.884
r_long_range_B_refined10.328
r_long_range_B_other10.326
r_scangle_other8.811
r_mcangle_other7.277
r_mcangle_it7.276
r_dihedral_angle_1_deg6.424
r_scbond_it6.339
r_scbond_other6.338
r_mcbond_it5.264
r_mcbond_other5.264
r_angle_refined_deg2.383
r_angle_other_deg0.784
r_chiral_restr0.12
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
r_dihedral_angle_4_deg
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24108
Nucleic Acid Atoms
Solvent Atoms664
Heterogen Atoms224

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing