6NFP | pdb_00006nfp

1.7 Angstrom Resolution Crystal Structure of Arginase from Bacillus subtilis subsp. subtilis str. 168


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CEV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5292Protein: 40.0 mg/ml, 0.3M Sodium chloride, 0.01M HEPES pH 7.5, Screen: 0.2M Magnesium chloride,0.1M Tris-HCL pH 8.5, 17% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.414α = 90
b = 143.989β = 109.35
c = 85.515γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.73094.50.0610.0610.0690.03220.34.4191464-327.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7395.30.7790.7790.8870.4210.6182.24.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2CEV1.729.99181718970694.30.14080.139460.150.166460.17RANDOM28.936
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]
2.790.21-1.37-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.291
r_dihedral_angle_4_deg16.191
r_dihedral_angle_3_deg9.849
r_long_range_B_refined6.263
r_long_range_B_other6.065
r_dihedral_angle_1_deg3.743
r_scangle_other3.511
r_scbond_it2.574
r_scbond_other2.574
r_mcangle_it2.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.291
r_dihedral_angle_4_deg16.191
r_dihedral_angle_3_deg9.849
r_long_range_B_refined6.263
r_long_range_B_other6.065
r_dihedral_angle_1_deg3.743
r_scangle_other3.511
r_scbond_it2.574
r_scbond_other2.574
r_mcangle_it2.118
r_mcangle_other2.118
r_mcbond_it1.377
r_angle_refined_deg1.373
r_mcbond_other1.366
r_angle_other_deg0.366
r_chiral_restr0.07
r_gen_planes_refined0.056
r_gen_planes_other0.056
r_bond_refined_d0.006
r_bond_other_d0.001
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 Atoms13179
Nucleic Acid Atoms
Solvent Atoms1623
Heterogen Atoms314

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing