6XWK

Crystal structure of Phormidium rubidum phycocyanin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YJJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP294MPD, PEG1000, PEG3350, Diethylene glycol, Triethylene glycol, Tetraethylene glycol, Pentaethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.754.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.32α = 90
b = 106.32β = 90
c = 58.67γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.84920DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.1739.39100121.314127070
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.171.20.51

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4yjj1.1739.39127046616599.9730.120.11880.14515.305
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]
-0.981-0.491-0.9813.184
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.319
r_dihedral_angle_other_3_deg33.699
r_dihedral_angle_4_deg20.377
r_dihedral_angle_3_deg12.875
r_dihedral_angle_1_deg4.83
r_rigid_bond_restr4.404
r_lrange_it3.81
r_lrange_other3.15
r_scangle_other3.127
r_scangle_it3.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.319
r_dihedral_angle_other_3_deg33.699
r_dihedral_angle_4_deg20.377
r_dihedral_angle_3_deg12.875
r_dihedral_angle_1_deg4.83
r_rigid_bond_restr4.404
r_lrange_it3.81
r_lrange_other3.15
r_scangle_other3.127
r_scangle_it3.126
r_scbond_it2.454
r_scbond_other2.453
r_mcangle_it1.853
r_mcangle_other1.833
r_angle_refined_deg1.747
r_angle_other_deg1.71
r_mcbond_it1.58
r_mcbond_other1.56
r_symmetry_nbd_refined0.307
r_nbd_other0.279
r_nbd_refined0.231
r_symmetry_xyhbond_nbd_refined0.202
r_symmetry_nbd_other0.186
r_xyhbond_nbd_refined0.186
r_nbtor_refined0.18
r_symmetry_xyhbond_nbd_other0.131
r_chiral_restr0.101
r_symmetry_nbtor_other0.086
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2484
Nucleic Acid Atoms
Solvent Atoms463
Heterogen Atoms190

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing