4GVZ

Crystal structure of arginine kinase in complex with D-arginine, MgADP, and nitrate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M15PDB ENTRY 1M15

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.2445.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.109α = 90
b = 65.382β = 90
c = 85.912γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2002-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R1.541

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.95835.90193.947468746811

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 1M152.9635.917468746821993.90.1940.1920.229
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]
0.9878-10.4635-4.2481
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.92
f_angle_d0.758
f_chiral_restr0.058
f_plane_restr0.004
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2817
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms44

Software

Software
Software NamePurpose
CrystalCleardata collection
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing