3IIU

Structure of the reconstituted Peridinin-Chlorophyll a-Protein (RFPCP) mutant N89L


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IISPDB ENTRY 3IIS RFPCP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.62960.1M CdCl2, 0,1M Sodium Acetate pH 4.6, 20-24% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
3.362.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.51α = 90
b = 81.73β = 90
c = 75.33γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102008-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9334ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4543.0799.90.11716.411.93777137771-3-316.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.451.5599.90.564.9911.076721

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3IIS RFPCP1.4543.07377713777118891000.155660.155660.154560.17648RANDOM12.356
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]
-0.20.010.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.447
r_dihedral_angle_3_deg12.834
r_dihedral_angle_4_deg5.163
r_dihedral_angle_1_deg4.368
r_angle_refined_deg3.295
r_scangle_it3.278
r_scbond_it2.242
r_mcangle_it1.337
r_mcbond_it0.79
r_chiral_restr0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.447
r_dihedral_angle_3_deg12.834
r_dihedral_angle_4_deg5.163
r_dihedral_angle_1_deg4.368
r_angle_refined_deg3.295
r_scangle_it3.278
r_scbond_it2.242
r_mcangle_it1.337
r_mcbond_it0.79
r_chiral_restr0.24
r_bond_refined_d0.017
r_gen_planes_refined0.016
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1120
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms326

Software

Software
Software NamePurpose
XDSdata scaling
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling