4ZV1

An ancestral arginine-binding protein bound to arginine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1WDN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52770.2 M Li2SO4, 0.1 M HEPES pH 7.5, 27.5% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5351.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.46α = 90
b = 60.41β = 90
c = 103.99γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2013-10-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.9537Australian SynchrotronMX1

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
11.5228.5699.60.093126.940887
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)
11.521.5594.40.6122.44.7

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 REPLACEMENTTHROUGHOUT1WDN1.5228.5638763205299.480.171540.169980.2005RANDOM14.732
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.19
r_dihedral_angle_3_deg13.924
r_dihedral_angle_4_deg10.157
r_long_range_B_refined6.702
r_long_range_B_other6.425
r_dihedral_angle_1_deg6.341
r_scangle_other4.313
r_scbond_it2.84
r_scbond_other2.84
r_mcangle_it2.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.19
r_dihedral_angle_3_deg13.924
r_dihedral_angle_4_deg10.157
r_long_range_B_refined6.702
r_long_range_B_other6.425
r_dihedral_angle_1_deg6.341
r_scangle_other4.313
r_scbond_it2.84
r_scbond_other2.84
r_mcangle_it2.549
r_mcangle_other2.548
r_angle_refined_deg2.318
r_mcbond_it1.691
r_mcbond_other1.691
r_angle_other_deg0.938
r_chiral_restr0.133
r_bond_refined_d0.024
r_gen_planes_refined0.011
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1728
Nucleic Acid Atoms
Solvent Atoms308
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing