3MHD

Crystal structure of DCR3


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52900.2M sodium acetate, 1mM CaCl2, 0.1M sodium citrate, 10% PEG 4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.9168.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.019α = 90
b = 130.019β = 90
c = 96.026γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9791NSLSX29A

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
12.7500.07318.97.386778677
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)
2.72.80.7931.25.7859

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 3K512.90120601016988.170.286190.285350.31481RANDOM86.336
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]
0.950.470.95-1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.428
r_dihedral_angle_3_deg19.838
r_scangle_it16.004
r_dihedral_angle_4_deg14.289
r_scbond_it10.879
r_dihedral_angle_1_deg7.869
r_mcangle_it6.649
r_mcbond_it4.144
r_angle_refined_deg1.212
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.428
r_dihedral_angle_3_deg19.838
r_scangle_it16.004
r_dihedral_angle_4_deg14.289
r_scbond_it10.879
r_dihedral_angle_1_deg7.869
r_mcangle_it6.649
r_mcbond_it4.144
r_angle_refined_deg1.212
r_nbtor_refined0.301
r_xyhbond_nbd_refined0.137
r_nbd_refined0.129
r_symmetry_vdw_refined0.104
r_chiral_restr0.089
r_symmetry_hbond_refined0.033
r_bond_refined_d0.008
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 Atoms1004
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
CBASSdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling