4R51

Crystal complex structure of sp-Aspartate-Semialdehyde-Dehydrogenase with Nicotinamide Adenine dinucleotide phosphate and phthalic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PWK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529515-22% PEG 3350, 0.1 M Na-acetate, 0.1 M MES (pH 6.5), 10mM TCEP, 3% Ethylene Glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.2946.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.78α = 90
b = 98.399β = 102.65
c = 63.973γ = 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 mirrors2013-07-29MSINGLE 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
11.85098.80.1517.836569064905223.4
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)
11.81.8698.70.5282.42.76446

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3PWK1.8150261525328398.060.176890.175750.19775RANDOM25.955
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]
0.530.98-1.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.524
r_dihedral_angle_4_deg17.974
r_dihedral_angle_3_deg13.115
r_dihedral_angle_1_deg5.827
r_long_range_B_refined4.16
r_long_range_B_other4.074
r_scangle_other2.663
r_mcangle_it1.762
r_mcangle_other1.762
r_scbond_it1.643
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.524
r_dihedral_angle_4_deg17.974
r_dihedral_angle_3_deg13.115
r_dihedral_angle_1_deg5.827
r_long_range_B_refined4.16
r_long_range_B_other4.074
r_scangle_other2.663
r_mcangle_it1.762
r_mcangle_other1.762
r_scbond_it1.643
r_scbond_other1.643
r_angle_refined_deg1.281
r_mcbond_it1.096
r_mcbond_other1.095
r_angle_other_deg0.746
r_chiral_restr0.07
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5388
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms155

Software

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