2GNU

The crystallization of reaction center from Rhodobacter sphaeroides occurs via a new route


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OGVPDB entry 1OGV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.129320% jeffamine M600, 1M HEPES, 0.7M (NH4)2SO4, 2.5% 1,2,3-heptanetriol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2862.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.422α = 90
b = 100.422β = 90
c = 235.412γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.2117.85199.80.1170.1175.610.261848
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.321000.6410.6410.94.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1OGV2.219.861641312999.570.2020.20.246RANDOM26.641
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]
0.030.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg21.447
r_dihedral_angle_3_deg17.782
r_dihedral_angle_1_deg6.176
r_scangle_it3.249
r_angle_refined_deg2.658
r_scbond_it2.091
r_mcangle_it1.627
r_mcbond_it1.004
r_nbtor_refined0.317
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.404
r_dihedral_angle_4_deg21.447
r_dihedral_angle_3_deg17.782
r_dihedral_angle_1_deg6.176
r_scangle_it3.249
r_angle_refined_deg2.658
r_scbond_it2.091
r_mcangle_it1.627
r_mcbond_it1.004
r_nbtor_refined0.317
r_nbd_refined0.227
r_symmetry_vdw_refined0.212
r_chiral_restr0.166
r_symmetry_hbond_refined0.15
r_xyhbond_nbd_refined0.145
r_bond_refined_d0.02
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6419
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms471

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling