9FHN | pdb_00009fhn

Crystal structure of the arginine kinase Der p 20.0101


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH2930.2 M Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.1843.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.28α = 90
b = 99.02β = 108.056
c = 77.883γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELBruker PHOTON III2022-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1LIQUID ANODEExcillum MetalJet D2+ 70 kV1.34138

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.959.390.80.1440.9784.32.949720
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.940.50.708

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.959.340075204473.1060.2720.26970.26950.30980.30987.484
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]
0.213-0.4441.494-1.169
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.146
r_dihedral_angle_3_deg14.45
r_dihedral_angle_2_deg6.974
r_dihedral_angle_1_deg6.679
r_angle_refined_deg1.232
r_lrange_it1.087
r_lrange_other1.059
r_scangle_it0.592
r_scangle_other0.592
r_mcangle_it0.586
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.146
r_dihedral_angle_3_deg14.45
r_dihedral_angle_2_deg6.974
r_dihedral_angle_1_deg6.679
r_angle_refined_deg1.232
r_lrange_it1.087
r_lrange_other1.059
r_scangle_it0.592
r_scangle_other0.592
r_mcangle_it0.586
r_mcangle_other0.586
r_angle_other_deg0.425
r_mcbond_it0.409
r_mcbond_other0.409
r_scbond_it0.394
r_scbond_other0.394
r_symmetry_xyhbond_nbd_refined0.35
r_nbd_other0.244
r_xyhbond_nbd_refined0.243
r_symmetry_nbd_refined0.221
r_nbd_refined0.22
r_symmetry_nbd_other0.207
r_nbtor_refined0.176
r_symmetry_xyhbond_nbd_other0.151
r_ncsr_local_group_10.088
r_symmetry_nbtor_other0.077
r_chiral_restr0.058
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5580
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing