3LZZ

Crystal structures of Cupin superfamily BbDUF985 from Branchiostoma belcheri tsingtauense in apo and GDP-bound forms


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62892.0M ammonium sulfate, 0.1M sodium acetate trihydate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K
Crystal Properties
Matthews coefficientSolvent content
4.2471.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.86α = 90
b = 88.86β = 90
c = 168.17γ = 90
Symmetry
Space GroupI 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2009-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
12.584.2298.60.05315.62.72216856.3
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)
2.52.6498.90.3713.12.73223

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 REPLACEMENTTHROUGHOUT1YUD2.519.9420964112598.120.200540.198350.24125RANDOM35.993
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]
1.121.12-2.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.083
r_dihedral_angle_3_deg16.887
r_dihedral_angle_4_deg15.773
r_dihedral_angle_1_deg7.389
r_scangle_it5.836
r_scbond_it3.561
r_mcangle_it2.233
r_angle_refined_deg2.067
r_mcbond_it1.149
r_chiral_restr0.139
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.083
r_dihedral_angle_3_deg16.887
r_dihedral_angle_4_deg15.773
r_dihedral_angle_1_deg7.389
r_scangle_it5.836
r_scbond_it3.561
r_mcangle_it2.233
r_angle_refined_deg2.067
r_mcbond_it1.149
r_chiral_restr0.139
r_bond_refined_d0.023
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms2588
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms64

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling