2VJH

The structure of Phycoerythrin from Gloeobacter violaceus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B8DPDB ENTRY 1B8D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110% W/V PEG 8K, 0.33 M SODIUM CACODYLATE, 0.67 M MAGNESIUM CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
240

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.829α = 90
b = 155.829β = 90
c = 155.829γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.1SRSPX10.1

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
12.1944.991000.1319.5314.0664149
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)
12.192.211000.344.289.23

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1B8D2.243.236080132391000.1550.1530.186RANDOM22.9
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.594
r_dihedral_angle_4_deg14.039
r_dihedral_angle_3_deg12.998
r_dihedral_angle_1_deg5.058
r_scangle_it2.8
r_angle_refined_deg2.328
r_scbond_it1.984
r_angle_other_deg1.183
r_mcangle_it1.056
r_mcbond_it0.929
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.594
r_dihedral_angle_4_deg14.039
r_dihedral_angle_3_deg12.998
r_dihedral_angle_1_deg5.058
r_scangle_it2.8
r_angle_refined_deg2.328
r_scbond_it1.984
r_angle_other_deg1.183
r_mcangle_it1.056
r_mcbond_it0.929
r_symmetry_vdw_other0.249
r_nbd_refined0.207
r_nbd_other0.199
r_nbtor_refined0.173
r_symmetry_hbond_refined0.144
r_xyhbond_nbd_refined0.14
r_symmetry_vdw_refined0.112
r_nbtor_other0.092
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_other0.012
r_gen_planes_refined0.008
r_bond_other_d0.005
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5054
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms430

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing