2AV6

X-Ray studies on maltodextrin phosphorylase complexes: recognition of substrates and cathalitic mechanism of phosphorylase family


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L5VPDB ENTRY 1L5V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298PEG4000, Lithium chloride, TRIS (hydroxymethil) aminomethane, maltopentaose, alluminium nitrate, sodium fluoride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.448.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.957α = 90
b = 105.614β = 90
c = 218.629γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.2ELETTRA5.2R

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
12.01111.80.1496.72.110216110061321.8
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)
12.012.110.44721.910682

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1L5V2.011595530505886.290.19270.189980.24387RANDOM24.683
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]
-0.97-1.152.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.59
r_scangle_it3.898
r_angle_other_deg3.762
r_scbond_it2.407
r_angle_refined_deg1.667
r_mcangle_it1.501
r_mcbond_it0.85
r_symmetry_vdw_other0.327
r_nbd_other0.281
r_nbd_refined0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.59
r_scangle_it3.898
r_angle_other_deg3.762
r_scbond_it2.407
r_angle_refined_deg1.667
r_mcangle_it1.501
r_mcbond_it0.85
r_symmetry_vdw_other0.327
r_nbd_other0.281
r_nbd_refined0.22
r_symmetry_vdw_refined0.188
r_symmetry_hbond_refined0.166
r_xyhbond_nbd_refined0.164
r_nbtor_other0.109
r_chiral_restr0.107
r_bond_refined_d0.02
r_gen_planes_other0.011
r_gen_planes_refined0.008
r_bond_other_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12778
Nucleic Acid Atoms
Solvent Atoms1145
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling