3G7F

Crystal structure of Blastochloris viridis heterodimer mutant reaction center


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I5NPDB entry 2i5n

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6298Plug-based microfluidics, Precipitant was mixed with buffer and RC sample in a microfluidic chip. The final precipitant concentration was ~1.7 M ammonium sulfate, 0.1% LDAO,30 mM NaH2PO4-Na2HPO4, pH 6.0, 3% 1,2,3-heptanetriol, 1.9% triethylammonium phosphate. RC concentration was ~ 9.4 mg/mL, Microbatch, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 220.132α = 90
b = 220.132β = 90
c = 112.744γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-CAPS14-BM-C

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
12.5500.1377.195377
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)
12.52.590.7096.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2i5n2.52090386476599.210.177260.175740.20556RANDOM31.995
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]
0.340.34-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.108
r_dihedral_angle_4_deg17.105
r_dihedral_angle_3_deg14.436
r_dihedral_angle_1_deg5.626
r_scangle_it2.672
r_scbond_it1.76
r_angle_refined_deg1.503
r_mcangle_it1.186
r_mcbond_it0.667
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.108
r_dihedral_angle_4_deg17.105
r_dihedral_angle_3_deg14.436
r_dihedral_angle_1_deg5.626
r_scangle_it2.672
r_scbond_it1.76
r_angle_refined_deg1.503
r_mcangle_it1.186
r_mcbond_it0.667
r_nbtor_refined0.314
r_symmetry_vdw_refined0.251
r_nbd_refined0.21
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.143
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9278
Nucleic Acid Atoms
Solvent Atoms730
Heterogen Atoms909

Software

Software
Software NamePurpose
HKL-2000data collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing