5HD2

The crystal structure of SeMet-Cry51Aa2-L11M


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293Starting protein solution was 5.5 mg/ml protein in 25 mM sodium carbonate buffer-pH 10.5. The reservoir solution was 500 ul of 2.0 M sodium chloride and 50 mM HEPES-pH 7.5 buffer. Bipyramidal crystals resulted from 2 ul drops, using 0.7 ul protein solution and 1.3 ul well solution.
Crystal Properties
Matthews coefficientSolvent content
2.3748

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.567α = 90
b = 55.567β = 90
c = 208.962γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate115 data frames were collected using 3 second exposures, with an oscillation angle of 1 degree, and a crystal-to-detector distance of 200 mm.2007-12-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.000APS21-ID-D

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
12.2753.795.90.09417.44.71523615236
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)
12.272.3596.40.3811.754.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.27653.71453176696.060.238130.235230.29458RANDOM41.305
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]
1.241.24-2.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.353
r_dihedral_angle_3_deg21.268
r_dihedral_angle_4_deg21.028
r_dihedral_angle_1_deg7.883
r_scangle_it4.674
r_scbond_it3.001
r_mcangle_it1.917
r_angle_refined_deg1.798
r_mcbond_it1.047
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.353
r_dihedral_angle_3_deg21.268
r_dihedral_angle_4_deg21.028
r_dihedral_angle_1_deg7.883
r_scangle_it4.674
r_scbond_it3.001
r_mcangle_it1.917
r_angle_refined_deg1.798
r_mcbond_it1.047
r_chiral_restr0.126
r_bond_refined_d0.019
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_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 Atoms2390
Nucleic Acid Atoms
Solvent Atoms47
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing