2Q30

Crystal structure of a rmlc-like cupin protein (dde_2303) from desulfovibrio desulfuricans subsp. at 1.94 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293NANODROP, 35.0% PEG 3000, 0.2M Sodium chloride, 0.1M Tris-HCl pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2VAPOR DIFFUSION, SITTING DROP8293NANODROP, 40.0% PEG 3000, 0.2M Sodium chloride, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.14α = 90
b = 133.95β = 93.04
c = 74.66γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-09-10MSINGLE WAVELENGTH
22x-ray100CCDADSC QUANTUM 315Vertically collimating premirror, toroidal focusing hexapod mirror2006-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.31.00000ALS5.0.3
2SYNCHROTRONALS BEAMLINE 5.0.20.98030ALS5.0.2

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
1,21.9429.02581.50.068.4560310-329.144
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)
1,21.942.01570.3172.5

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 DIFFRACTIONSADTHROUGHOUT1.9429.02560283317396.410.1690.1670.212RANDOM26.755
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]
0.160.8-2.051.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.767
r_dihedral_angle_4_deg17.609
r_dihedral_angle_3_deg10.34
r_scangle_it6.636
r_scbond_it4.724
r_dihedral_angle_1_deg4.561
r_mcangle_it2.306
r_mcbond_it1.951
r_angle_refined_deg1.791
r_angle_other_deg1.288
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.767
r_dihedral_angle_4_deg17.609
r_dihedral_angle_3_deg10.34
r_scangle_it6.636
r_scbond_it4.724
r_dihedral_angle_1_deg4.561
r_mcangle_it2.306
r_mcbond_it1.951
r_angle_refined_deg1.791
r_angle_other_deg1.288
r_mcbond_other0.584
r_nbd_refined0.16
r_nbtor_refined0.153
r_symmetry_vdw_other0.151
r_nbd_other0.149
r_symmetry_hbond_refined0.116
r_symmetry_vdw_refined0.108
r_chiral_restr0.105
r_xyhbond_nbd_refined0.105
r_nbtor_other0.077
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6366
Nucleic Acid Atoms
Solvent Atoms654
Heterogen Atoms33

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
SHARPphasing