2OP5

CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (JCVI_PEP_1096672785533) FROM UNCULTURED MARINE ORGANISM AT 2.20 A RESOLUTION


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.3277NANODROP, 0.2M Potassium formate, 20.0% PEG 3350, No Buffer, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0740.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.558α = 90
b = 84.629β = 90
c = 144.952γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focusing mirrors in K-B geometry2006-10-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.94645, 0.97942, 0.97921APS23-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
12.248.3499.60.157.223608225.76
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)
12.22.2898.80.6831.83630

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.248.3436027179999.670.2330.2330.230.292RANDOM27.408
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]
0.431.26-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.52
r_dihedral_angle_4_deg16.868
r_dihedral_angle_3_deg11.613
r_dihedral_angle_1_deg3.367
r_scangle_it2.561
r_scbond_it1.764
r_angle_refined_deg1.51
r_mcangle_it1.371
r_mcbond_it0.904
r_angle_other_deg0.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.52
r_dihedral_angle_4_deg16.868
r_dihedral_angle_3_deg11.613
r_dihedral_angle_1_deg3.367
r_scangle_it2.561
r_scbond_it1.764
r_angle_refined_deg1.51
r_mcangle_it1.371
r_mcbond_it0.904
r_angle_other_deg0.863
r_mcbond_other0.211
r_xyhbond_nbd_refined0.195
r_symmetry_hbond_refined0.192
r_nbd_refined0.183
r_nbtor_refined0.183
r_nbd_other0.158
r_symmetry_vdw_other0.151
r_symmetry_vdw_refined0.144
r_chiral_restr0.085
r_nbtor_other0.085
r_xyhbond_nbd_other0.028
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5307
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms36

Software

Software
Software NamePurpose
MolProbitymodel building
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing