2ASV

X-Ray studies on protein complexes: Enzymatic catalysis in Crystals of E. coli Maltodextrin Phosphorylase (MalP)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L5Vpdb entry 1L5V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298PEG 4000, lithium chloride, (hydroxymethyl) aminomethane, maltopentaose, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.346.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.327α = 90
b = 104.723β = 90
c = 214.787γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrors2004-03-31MSINGLE 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
11.951597.80.11910.13.912174411984925.9
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)
11.952.0691.10.4761.82.716075

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 1L5V1.9515113766601897.460.181680.179390.22604RANDOM30.275
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]
-0.8-11.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.442
r_scangle_it4.099
r_angle_other_deg3.679
r_scbond_it2.534
r_angle_refined_deg1.633
r_mcangle_it1.568
r_mcbond_it0.88
r_symmetry_vdw_other0.325
r_nbd_other0.286
r_symmetry_vdw_refined0.253
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.442
r_scangle_it4.099
r_angle_other_deg3.679
r_scbond_it2.534
r_angle_refined_deg1.633
r_mcangle_it1.568
r_mcbond_it0.88
r_symmetry_vdw_other0.325
r_nbd_other0.286
r_symmetry_vdw_refined0.253
r_nbd_refined0.225
r_symmetry_hbond_refined0.184
r_xyhbond_nbd_refined0.164
r_nbtor_other0.11
r_chiral_restr0.105
r_bond_refined_d0.019
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 Atoms1184
Heterogen Atoms174

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
CCP4data scaling