8RVK

Maltodextrin phosphorylase (MalP) in complex with a alpha-1,2-cyclophellitol analogue


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2-0.5 M Li2SO4 monohydrate, 0.1 M Bis-Tris pH 5.5-7.0 and 25-30% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7555.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.498α = 90
b = 119.79β = 90
c = 150.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.8971.50399.90.9925.91.9160021
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.891.9297.10.2840.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTNONE2.1871.503159923137799.9920.1780.17730.229436.046
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]
2.095-1.845-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.369
r_dihedral_angle_6_deg15.704
r_dihedral_angle_2_deg12.402
r_lrange_other8.268
r_lrange_it8.266
r_scangle_it7.713
r_scangle_other7.395
r_dihedral_angle_1_deg7.25
r_scbond_it5.817
r_mcangle_other5.743
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.369
r_dihedral_angle_6_deg15.704
r_dihedral_angle_2_deg12.402
r_lrange_other8.268
r_lrange_it8.266
r_scangle_it7.713
r_scangle_other7.395
r_dihedral_angle_1_deg7.25
r_scbond_it5.817
r_mcangle_other5.743
r_mcangle_it5.741
r_scbond_other5.617
r_mcbond_it4.589
r_mcbond_other4.583
r_angle_refined_deg2.381
r_angle_other_deg0.842
r_symmetry_xyhbond_nbd_refined0.288
r_nbd_refined0.232
r_nbd_other0.228
r_symmetry_nbd_other0.206
r_symmetry_nbd_refined0.202
r_nbtor_refined0.193
r_xyhbond_nbd_refined0.172
r_chiral_restr0.132
r_symmetry_xyhbond_nbd_other0.095
r_ncsr_local_group_10.095
r_symmetry_nbtor_other0.09
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12599
Nucleic Acid Atoms
Solvent Atoms630
Heterogen Atoms312

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata scaling
Cootmodel building
MOLREPphasing
xia2data reduction