2OD4

Crystal structure of a dimeric ferredoxin-like protein (jcvi_pep_1096665735785) from uncultured marine organism at 1.70 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP, NANODROP4.52770.2M Li2SO4, 2.5M NaCl, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.2645.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 31.89α = 90
b = 77.79β = 102.66
c = 43.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2006-11-19MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837, 0.97966SSRLBL11-1

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
11.728.89298.30.0616.762279721.1
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)
11.71.76990.4032.02

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 DIFFRACTIONMADTHROUGHOUT1.728.89222774117299.110.1610.1590.193RANDOM20.689
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]
2.630.35-0.97-1.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.483
r_dihedral_angle_4_deg17.156
r_dihedral_angle_3_deg13.235
r_scangle_it7.614
r_dihedral_angle_1_deg5.445
r_scbond_it5.384
r_mcangle_it2.832
r_mcbond_it2.427
r_angle_refined_deg1.415
r_angle_other_deg0.881
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.483
r_dihedral_angle_4_deg17.156
r_dihedral_angle_3_deg13.235
r_scangle_it7.614
r_dihedral_angle_1_deg5.445
r_scbond_it5.384
r_mcangle_it2.832
r_mcbond_it2.427
r_angle_refined_deg1.415
r_angle_other_deg0.881
r_mcbond_other0.503
r_symmetry_vdw_other0.285
r_symmetry_vdw_refined0.261
r_nbd_refined0.215
r_nbd_other0.188
r_nbtor_refined0.187
r_xyhbond_nbd_refined0.175
r_symmetry_hbond_refined0.145
r_nbtor_other0.087
r_chiral_restr0.086
r_bond_refined_d0.015
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1619
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms8

Software

Software
Software NamePurpose
MolProbitymodel building
SOLVEphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction