3VZG

Crystal structure of human pancreatic secretory protein ZG16p with O-(alpha-D-mannosyl)-L-threonine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3APA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.62930.09M MES(pH 6.5), 0.09M Sodium phosphate, 0.09M Potassium phosphate, 1.8M Sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.0941.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.397α = 90
b = 73.022β = 90
c = 30.4γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102011-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5APhoton FactoryBL-5A

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
12.75098.30.117.56.83909
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)
12.72.751000.3454.86.6

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 REPLACEMENTTHROUGHOUT3APA2.745.6366017098.60.220.2170.288RANDOM27.43
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]
-1.11-0.92.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.411
r_dihedral_angle_4_deg14.706
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg4.632
r_angle_refined_deg0.827
r_scangle_it0.392
r_nbtor_refined0.296
r_mcangle_it0.238
r_scbond_it0.221
r_nbd_refined0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.411
r_dihedral_angle_4_deg14.706
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg4.632
r_angle_refined_deg0.827
r_scangle_it0.392
r_nbtor_refined0.296
r_mcangle_it0.238
r_scbond_it0.221
r_nbd_refined0.14
r_mcbond_it0.129
r_symmetry_vdw_refined0.094
r_xyhbond_nbd_refined0.081
r_chiral_restr0.047
r_symmetry_hbond_refined0.04
r_bond_refined_d0.005
r_gen_planes_refined0.002
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 Atoms1084
Nucleic Acid Atoms
Solvent Atoms51
Heterogen Atoms21

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALAdata scaling