2AZD

X-Ray studies on Maltodextrin Phosphorylase (MalP) Complexes: recognition of substrates and CATALYTIC mechanism of phosphorylase family


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298PEG4000, lithium chloride, TRIS (HYDROXYMETHIL)AMINOMETHANE, MALTOPENTAOSE, SODIUM ORTHOVANADATE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.779α = 90
b = 105.892β = 90
c = 220.23γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE 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
12.16111.80.13212.66.5962108891134.35
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)
12.162.280.7092.25.812410

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.166.8384393445891.540.2070.204680.24967RANDOM35.91
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]
0.09-0.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.979
r_scangle_it4.163
r_scbond_it2.598
r_angle_refined_deg1.887
r_mcangle_it1.787
r_angle_other_deg1.187
r_mcbond_it1.003
r_symmetry_vdw_other0.297
r_nbd_other0.255
r_nbd_refined0.225
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.979
r_scangle_it4.163
r_scbond_it2.598
r_angle_refined_deg1.887
r_mcangle_it1.787
r_angle_other_deg1.187
r_mcbond_it1.003
r_symmetry_vdw_other0.297
r_nbd_other0.255
r_nbd_refined0.225
r_symmetry_hbond_refined0.222
r_symmetry_vdw_refined0.213
r_xyhbond_nbd_refined0.194
r_chiral_restr0.116
r_nbtor_other0.094
r_bond_refined_d0.025
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12778
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms146

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing