5NB4

Atomic resolution structure of C-phycoerythrin from marine cyanobacterium Phormidium sp. A09DM at pH 7.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AQD 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5294.15Morpheus screen condition C8 with the NPS mix of additives
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.046α = 78.78
b = 109.095β = 82.32
c = 117.371γ = 60.26
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97951DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.1494.6293.80.0420.0420.99810.72.615752269.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.141.16900.5450.5450.6011.62.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT5aqd1.1494.6214960037918893.80.1490.1470.184RANDOM15.58
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]
-0.070.11-0.47-0.50.090.95
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.964
r_dihedral_angle_2_deg34.428
r_dihedral_angle_4_deg17.023
r_dihedral_angle_3_deg12.897
r_sphericity_bonded12.278
r_long_range_B_refined5.975
r_dihedral_angle_1_deg5.071
r_long_range_B_other4.31
r_mcangle_it3.105
r_mcangle_other3.105
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.964
r_dihedral_angle_2_deg34.428
r_dihedral_angle_4_deg17.023
r_dihedral_angle_3_deg12.897
r_sphericity_bonded12.278
r_long_range_B_refined5.975
r_dihedral_angle_1_deg5.071
r_long_range_B_other4.31
r_mcangle_it3.105
r_mcangle_other3.105
r_angle_refined_deg2.682
r_scangle_other2.589
r_mcbond_it2.45
r_mcbond_other2.45
r_scbond_it2.229
r_scbond_other2.219
r_rigid_bond_restr2.203
r_angle_other_deg1.216
r_chiral_restr0.114
r_gen_planes_other0.018
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.004
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 Atoms31032
Nucleic Acid Atoms
Solvent Atoms8168
Heterogen Atoms2836

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata collection
Aimlessdata scaling
Cootmodel building
REFMACphasing