2I5N

1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DXRPDB ENTRY 1DXR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1THE CRYSTALS WERE GROWN BY MICROFLUIDIC TECHNIQUE USING CRYSTALLIZATION BUFFER: 1.6 - 1.8 M (NH4)2SO4 IN TRIS PH 7.8. THE ADDITIVES WERE HEPTANETRIOL (3%, W/V) AND 2% TRIETHYL AMONIUM PHOSPHATE. THE DETERGENT WAS LAURYL DIMETHYLAMINE-N-OXIDE (LDA). THE PROTEIN COMPLEX WAS IN SODIUM PHOSPHATE BUFFER PH 6.0 AND 0.08% LDA.
Crystal Properties
Matthews coefficientSolvent content
570

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 220.4α = 90
b = 220.4β = 90
c = 113.009γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUSING MIRRORS2006-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-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
11.962094.50.08217.55.918918924.5
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)
11.96267.40.482.34.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 1DXR1.9620189189189189953396.50.1730.1720.19RANDOM25.42
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]
0.350.35-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.902
r_dihedral_angle_4_deg16.534
r_dihedral_angle_3_deg12.261
r_dihedral_angle_1_deg5.683
r_scangle_it3.506
r_scbond_it2.507
r_mcangle_it1.659
r_angle_refined_deg1.329
r_mcbond_it1.117
r_angle_other_deg1.055
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.902
r_dihedral_angle_4_deg16.534
r_dihedral_angle_3_deg12.261
r_dihedral_angle_1_deg5.683
r_scangle_it3.506
r_scbond_it2.507
r_mcangle_it1.659
r_angle_refined_deg1.329
r_mcbond_it1.117
r_angle_other_deg1.055
r_mcbond_other0.32
r_symmetry_vdw_refined0.235
r_nbd_refined0.224
r_symmetry_vdw_other0.222
r_nbtor_refined0.203
r_nbd_other0.195
r_symmetry_hbond_refined0.124
r_xyhbond_nbd_refined0.114
r_nbtor_other0.085
r_chiral_restr0.065
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9282
Nucleic Acid Atoms
Solvent Atoms771
Heterogen Atoms970

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling