2BYG

2nd PDZ Domain of Discs Large Homologue 2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1825% PEG 3350, 0.2M NACL, 0.1M BIS-TRIS PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.244.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.774α = 90
b = 69.081β = 90
c = 73.967γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU-MSCOSMIC MIRRORS2005-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E

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
11.8534.5498.70.0419.94.19967
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)
11.851.9591.40.342.22.1

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 1PDR1.8550.51919575498.20.20.1960.252RANDOM35.84
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]
1.670.11-1.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.338
r_dihedral_angle_3_deg12.176
r_scangle_it8.567
r_scbond_it6.806
r_dihedral_angle_1_deg5.644
r_dihedral_angle_4_deg4.929
r_mcangle_it4.42
r_mcbond_it3.552
r_angle_refined_deg1.276
r_angle_other_deg0.704
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.338
r_dihedral_angle_3_deg12.176
r_scangle_it8.567
r_scbond_it6.806
r_dihedral_angle_1_deg5.644
r_dihedral_angle_4_deg4.929
r_mcangle_it4.42
r_mcbond_it3.552
r_angle_refined_deg1.276
r_angle_other_deg0.704
r_nbd_refined0.191
r_nbtor_refined0.17
r_nbd_other0.164
r_xyhbond_nbd_refined0.161
r_symmetry_vdw_other0.143
r_symmetry_hbond_refined0.126
r_symmetry_vdw_refined0.105
r_nbtor_other0.078
r_chiral_restr0.071
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms738
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing