3IIR

Crystal Structure of Miraculin like protein from seeds of Murraya koenigii


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82936% PEG 8000, 0.1mM Tris-Cl pH 8.0, 0.08M Sodium Chloride, 0.08M Calcium Chloride, 8% Glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6152.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.795α = 90
b = 75.795β = 90
c = 150.848γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plate2006-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.92596.10.1460.1464.75.6103005858151.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.92.9599.90.4220.4224.73.8540

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 1AVA2.9102930047397.560.219850.216180.29452RANDOM27.074
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]
0.060.06-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.199
r_dihedral_angle_3_deg20.025
r_dihedral_angle_4_deg17.008
r_dihedral_angle_1_deg7.794
r_angle_refined_deg1.668
r_scangle_it1.534
r_scbond_it0.932
r_mcangle_it0.858
r_mcbond_it0.527
r_symmetry_vdw_refined0.336
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.199
r_dihedral_angle_3_deg20.025
r_dihedral_angle_4_deg17.008
r_dihedral_angle_1_deg7.794
r_angle_refined_deg1.668
r_scangle_it1.534
r_scbond_it0.932
r_mcangle_it0.858
r_mcbond_it0.527
r_symmetry_vdw_refined0.336
r_nbtor_refined0.319
r_symmetry_hbond_refined0.302
r_nbd_refined0.257
r_xyhbond_nbd_refined0.169
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.004
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 Atoms2916
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling