7OU1

Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OS3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52922% PEG8000, 20% PEG400, 5 mM Mg(CH3COO)2, 6 mM 3.0 mM sucrose monolaureate
Crystal Properties
Matthews coefficientSolvent content
2.5551.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.923α = 90
b = 91.308β = 97.111
c = 114.164γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2019-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.30.8950BESSY14.3

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
11.6545.65990.1340.99510418988821.54
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)
11.651.75980.6220.7952.24.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7OS31.6545.65189888100099.0480.190.18980.221716.259
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]
-0.9310.344-0.6711.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.435
r_dihedral_angle_4_deg14.74
r_dihedral_angle_3_deg13.289
r_dihedral_angle_1_deg6.404
r_lrange_it4.596
r_lrange_other4.545
r_scangle_it2.636
r_scangle_other2.636
r_scbond_it1.702
r_scbond_other1.702
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.435
r_dihedral_angle_4_deg14.74
r_dihedral_angle_3_deg13.289
r_dihedral_angle_1_deg6.404
r_lrange_it4.596
r_lrange_other4.545
r_scangle_it2.636
r_scangle_other2.636
r_scbond_it1.702
r_scbond_other1.702
r_mcangle_it1.697
r_mcangle_other1.687
r_angle_refined_deg1.645
r_angle_other_deg1.509
r_mcbond_it1.079
r_mcbond_other1.068
r_nbd_refined0.212
r_nbd_other0.211
r_symmetry_xyhbond_nbd_refined0.198
r_symmetry_nbd_other0.184
r_nbtor_refined0.16
r_symmetry_nbd_refined0.157
r_xyhbond_nbd_refined0.156
r_symmetry_xyhbond_nbd_other0.108
r_chiral_restr0.091
r_symmetry_nbtor_other0.082
r_ncsr_local_group_50.082
r_ncsr_local_group_60.079
r_ncsr_local_group_10.077
r_ncsr_local_group_40.077
r_ncsr_local_group_20.074
r_ncsr_local_group_30.058
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10372
Nucleic Acid Atoms
Solvent Atoms1403
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing