6GGP

Structure of the ligand-free form of truncated ArgBP (residues 20-233) from T. maritima


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PRS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Crystals grew in 16-20 mg/mL protein solution and in 30 % w/v PEG 8,000, 0.1 M Sodium cacodylate trihydrate (pH 6.5) and 0.2 M Sodium Acetate trihydrate.
Crystal Properties
Matthews coefficientSolvent content
2.3247.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.707α = 90
b = 71.063β = 90
c = 88.386γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.9464ESRFBM14

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
11.032095.941.313.7104443
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.031.05

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 REPLACEMENTTHROUGHOUT4PRS1.031510336496995.80.1380.1370.171RANDOM8.77
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]
0.070.02-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.25
r_dihedral_angle_4_deg23.454
r_dihedral_angle_3_deg12.95
r_sphericity_free12.697
r_dihedral_angle_1_deg6.256
r_scangle_it6.133
r_sphericity_bonded4.733
r_scbond_it4.41
r_mcangle_it2.849
r_angle_refined_deg2.183
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.25
r_dihedral_angle_4_deg23.454
r_dihedral_angle_3_deg12.95
r_sphericity_free12.697
r_dihedral_angle_1_deg6.256
r_scangle_it6.133
r_sphericity_bonded4.733
r_scbond_it4.41
r_mcangle_it2.849
r_angle_refined_deg2.183
r_rigid_bond_restr2.118
r_mcbond_it1.962
r_angle_other_deg1.134
r_mcbond_other0.982
r_chiral_restr0.138
r_bond_refined_d0.027
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1651
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms

Software

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