4R5M

Crystal structure of Vc-Aspartate beta-semialdehyde-dehydrogenase with NADP and 4-Nitro-2-Phosphono-Benzoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3Q0E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529515-20% PEG 3350, 0.1 M Na-citrate (pH 6.5), 0.1 M Na-acetate, 10 mM DTT, 3% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.6653.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.353α = 90
b = 107.353β = 90
c = 152.837γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDdouble crystal monochromator and K-B pair of biomorph mirrors2014-07-27MSINGLE 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
11.885097.70.12310.64.9730607138222
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)
11.881.9586.60.3863.54.8

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3Q0E1.8987.857306267739361098.840.170580.169160.19696RANDOM31.393
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]
-0.57-0.571.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.9
r_dihedral_angle_4_deg18.375
r_dihedral_angle_3_deg11.273
r_dihedral_angle_1_deg5.68
r_long_range_B_refined5.291
r_long_range_B_other4.916
r_scangle_other2.748
r_mcangle_it1.983
r_mcangle_other1.983
r_scbond_other1.694
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.9
r_dihedral_angle_4_deg18.375
r_dihedral_angle_3_deg11.273
r_dihedral_angle_1_deg5.68
r_long_range_B_refined5.291
r_long_range_B_other4.916
r_scangle_other2.748
r_mcangle_it1.983
r_mcangle_other1.983
r_scbond_other1.694
r_scbond_it1.688
r_mcbond_it1.267
r_mcbond_other1.264
r_angle_refined_deg1.25
r_angle_other_deg0.757
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5654
Nucleic Acid Atoms
Solvent Atoms601
Heterogen Atoms129

Software

Software
Software NamePurpose
REFMACrefinement