5V2C

RE-REFINEMENT OF CRYSTAL STRUCTURE OF PHOTOSYSTEM II COMPLEX


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ARC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION, RECRYSTALLIZATION6.12855% PEG1450, 20MM NACL, 10MM CACL2, 40MM MGSO4, 20MM MES BUFFER, PH 6.1, MICRO-BATCH METHOD UNDER OIL, TEMPERATURE 285K
Crystal Properties
Matthews coefficientSolvent content
3.4264.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.19α = 90
b = 228.51β = 90
c = 286.4γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2009-11-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
11.9178.6299.60.0621.575.5622012-3
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)
11.91.9799.70.7732.63

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 REPLACEMENTTHROUGHOUT3ARC1.9178.625916553120299.770.095160.091570.1628RANDOM39.479
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]
0.50.55-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free63.088
r_dihedral_angle_2_deg33.496
r_sphericity_bonded26.094
r_dihedral_angle_4_deg16.663
r_dihedral_angle_3_deg13.188
r_scangle_other9.515
r_long_range_B_refined8.902
r_long_range_B_other8.902
r_scbond_it8.265
r_scbond_other8.265
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free63.088
r_dihedral_angle_2_deg33.496
r_sphericity_bonded26.094
r_dihedral_angle_4_deg16.663
r_dihedral_angle_3_deg13.188
r_scangle_other9.515
r_long_range_B_refined8.902
r_long_range_B_other8.902
r_scbond_it8.265
r_scbond_other8.265
r_mcangle_it6
r_mcangle_other6
r_dihedral_angle_1_deg5.84
r_mcbond_it5.07
r_mcbond_other5.06
r_rigid_bond_restr3.683
r_angle_refined_deg3.27
r_angle_other_deg1.138
r_chiral_restr0.116
r_bond_refined_d0.021
r_gen_planes_refined0.013
r_gen_planes_other0.013
r_bond_other_d0.003
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms41395
Nucleic Acid Atoms
Solvent Atoms3787
Heterogen Atoms11954

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing