4R4J

Crystal structure of complex sp_ASADH with 3-carboxypropyl-phthalic acid and Nicotinamide Adenine dinucleotide phosphate


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 buffer (pH 6.5), 10mM TCEP, 3% Ethylene Glycole, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3447.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.925α = 90
b = 98.842β = 100.91
c = 64.329γ = 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 mirrors2014-07-27MSINGLE 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
11.55082.50.07326.12.31295901069171214.9
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)
11.51.5683.70.3232.310830

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 SYNTHESISTHROUGHOUT4R3N1.5150129590101648524692.510.152950.151030.18997RANDOM21.244
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]
0.51-0.521.22-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.537
r_dihedral_angle_4_deg23.049
r_sphericity_free20.376
r_dihedral_angle_3_deg11.839
r_sphericity_bonded8.267
r_dihedral_angle_1_deg5.958
r_long_range_B_refined2.999
r_long_range_B_other2.917
r_scangle_other2.772
r_scbond_it2.378
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.537
r_dihedral_angle_4_deg23.049
r_sphericity_free20.376
r_dihedral_angle_3_deg11.839
r_sphericity_bonded8.267
r_dihedral_angle_1_deg5.958
r_long_range_B_refined2.999
r_long_range_B_other2.917
r_scangle_other2.772
r_scbond_it2.378
r_scbond_other2.378
r_mcangle_it2.066
r_mcangle_other2.066
r_rigid_bond_restr2.044
r_mcbond_it1.787
r_mcbond_other1.787
r_angle_refined_deg1.339
r_angle_other_deg0.746
r_chiral_restr0.069
r_bond_refined_d0.006
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 Atoms5461
Nucleic Acid Atoms
Solvent Atoms470
Heterogen Atoms206

Software

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