4R54

Complex crystal structure of sp-Aspartate-Semialdehyde-Dehydrogenase with 3-carboxy-ethyl-phthalic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4R3N 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529515-22% PEG 3350, 0.1 M Na-acetate, 0.1 M MES (pH 6.5), 10 mM TCEP, 3% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3146.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.537α = 90
b = 98.806β = 101.16
c = 64.098γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDdouble crystal monochromator and K-B pair of biomorph mirrors2014-04-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.850990.12264.666237655751229.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.8797.30.8084.46404

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4R3N1.815026557562262330398.680.185650.183770.21946RANDOM38.715
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]
1.12.051.56-3.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.096
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg13.021
r_dihedral_angle_1_deg5.972
r_long_range_B_refined5.024
r_long_range_B_other5.024
r_scangle_other3.717
r_mcangle_it2.562
r_mcangle_other2.562
r_scbond_it2.401
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.096
r_dihedral_angle_4_deg19.531
r_dihedral_angle_3_deg13.021
r_dihedral_angle_1_deg5.972
r_long_range_B_refined5.024
r_long_range_B_other5.024
r_scangle_other3.717
r_mcangle_it2.562
r_mcangle_other2.562
r_scbond_it2.401
r_scbond_other2.4
r_mcbond_it1.829
r_mcbond_other1.826
r_angle_refined_deg1.377
r_angle_other_deg0.745
r_chiral_restr0.074
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5448
Nucleic Acid Atoms
Solvent Atoms262
Heterogen Atoms172

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling