2GVN

L-asparaginase from Erwinia carotovora in complex with aspartic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529512% MMEPEG 5000, 0.03% b-D-glucopiranoside, 0.02% sodium azide, 20 mm aspartic acid sodium salt, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2645.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.061α = 90
b = 135.88β = 90
c = 251.525γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmbent mirror2005-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A0.98EMBL/DESY, HAMBURGBW7A

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
11.92097.20.04831.33.7191790191790
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)
11.91.9288.10.2245.53.25744

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1ZCF1.914.99181808181808964797.250.2190.2060.2040.229RANDOM27.126
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]
0.210.01-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.566
r_scangle_it11.733
r_scbond_it8.793
r_dihedral_angle_3_deg8.356
r_dihedral_angle_4_deg8.299
r_mcangle_it6.164
r_mcbond_it5.571
r_dihedral_angle_1_deg2.689
r_angle_refined_deg0.941
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.566
r_scangle_it11.733
r_scbond_it8.793
r_dihedral_angle_3_deg8.356
r_dihedral_angle_4_deg8.299
r_mcangle_it6.164
r_mcbond_it5.571
r_dihedral_angle_1_deg2.689
r_angle_refined_deg0.941
r_nbtor_refined0.302
r_nbd_refined0.142
r_symmetry_hbond_refined0.116
r_xyhbond_nbd_refined0.11
r_symmetry_vdw_refined0.091
r_chiral_restr0.088
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19296
Nucleic Acid Atoms
Solvent Atoms2301
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing