3OZ2

Crystal structure of a geranylgeranyl bacteriochlorophyll reductase-like (Ta0516) from Thermoplasma acidophilum at 1.60 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527715.00% Glycerol, 8.50% iso-Propanol, 17.00% PEG-4000, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3547.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.59α = 90
b = 70.67β = 90
c = 117.85γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCD2008-02-01MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97920,0.97862SSRLBL11-1

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
11.645.25799.40.05213.1655071-320.479
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)
11.61.6499.60.4662.4

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 DIFFRACTIONMADTHROUGHOUT1.645.25755071279499.350.15390.1530.1706RANDOM29.0611
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]
-0.571.08-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.406
r_dihedral_angle_4_deg16.988
r_dihedral_angle_3_deg12.23
r_scangle_it6.476
r_dihedral_angle_1_deg6.32
r_scbond_it4.121
r_mcangle_it2.518
r_angle_refined_deg1.608
r_mcbond_it1.497
r_angle_other_deg0.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.406
r_dihedral_angle_4_deg16.988
r_dihedral_angle_3_deg12.23
r_scangle_it6.476
r_dihedral_angle_1_deg6.32
r_scbond_it4.121
r_mcangle_it2.518
r_angle_refined_deg1.608
r_mcbond_it1.497
r_angle_other_deg0.911
r_mcbond_other0.422
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3004
Nucleic Acid Atoms
Solvent Atoms332
Heterogen Atoms157

Software

Software
Software NamePurpose
SHELXphasing
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing