2NTP

Crystal structure of pectin methylesterase in complex with hexasaccharide VI


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52931.6 M Ammonium sulfate, 0.1 M MES pH 6.5, 10% v/v Dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.8556.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.091α = 90
b = 85β = 93.56
c = 97.325γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 225 mmmonochromator2006-02-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.10.90000SRSPX10.1

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
11.736.321000.065153.8912459124513.25
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)
11.71.791000.2824.63.8

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 1QJV1.736.3286652456899.990.185720.184090.21665RANDOM16.201
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]
-0.570.150.440.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.663
r_dihedral_angle_4_deg15.529
r_dihedral_angle_3_deg11.748
r_dihedral_angle_1_deg5.802
r_scangle_it1.981
r_scbond_it1.338
r_angle_refined_deg1.003
r_mcangle_it0.88
r_mcbond_it0.49
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.663
r_dihedral_angle_4_deg15.529
r_dihedral_angle_3_deg11.748
r_dihedral_angle_1_deg5.802
r_scangle_it1.981
r_scbond_it1.338
r_angle_refined_deg1.003
r_mcangle_it0.88
r_mcbond_it0.49
r_nbtor_refined0.306
r_nbd_refined0.173
r_symmetry_vdw_refined0.167
r_xyhbond_nbd_refined0.101
r_symmetry_hbond_refined0.098
r_chiral_restr0.066
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5218
Nucleic Acid Atoms
Solvent Atoms1038
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing