5I3Z

Erwinia chrysanthemi L-asparaginase E63Q mutation + Aspartic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O7J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52850.1M HEPES, pH 7.5 and 24% of PEG MME 2000
Crystal Properties
Matthews coefficientSolvent content
2.1643.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.893α = 90
b = 87.885β = 90
c = 175.992γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-10-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.008264APS21-ID-D

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
12.058897.20.1150.99716.885.974069-319.7
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)
12.052.1883.50.4854.08

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 REPLACEMENTTHROUGHOUT1O7J2.053069755356396.220.17570.17390.2093RANDOM20.93
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]
-1.160.520.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.368
r_dihedral_angle_4_deg15.767
r_dihedral_angle_3_deg12.829
r_dihedral_angle_1_deg6.142
r_mcangle_it2.624
r_mcbond_it1.649
r_mcbond_other1.648
r_angle_refined_deg1.584
r_angle_other_deg1.299
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.368
r_dihedral_angle_4_deg15.767
r_dihedral_angle_3_deg12.829
r_dihedral_angle_1_deg6.142
r_mcangle_it2.624
r_mcbond_it1.649
r_mcbond_other1.648
r_angle_refined_deg1.584
r_angle_other_deg1.299
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_bond_other_d0.008
r_gen_planes_other0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9784
Nucleic Acid Atoms
Solvent Atoms976
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction