2YBV

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RUBPDB ENTRY 3RUB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
175% PEG8000, 20% PEG200, 10% GLYCEROL, 100MM HEPES, PH 7
Crystal Properties
Matthews coefficientSolvent content
2.7254

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.48α = 90
b = 163.47β = 108.96
c = 163.54γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2007-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
12.33999.90.1711.117.3253864
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)
12.32.3699.80.433.84.2

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 3RUB2.339.84240880129921000.197630.195770.23167RANDOM18.196
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]
1.450.69-0.77-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.881
r_dihedral_angle_3_deg14.816
r_dihedral_angle_4_deg14.538
r_dihedral_angle_1_deg6.63
r_scangle_it4.279
r_scbond_it2.661
r_angle_refined_deg1.782
r_mcangle_it1.756
r_mcbond_it0.9
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.881
r_dihedral_angle_3_deg14.816
r_dihedral_angle_4_deg14.538
r_dihedral_angle_1_deg6.63
r_scangle_it4.279
r_scbond_it2.661
r_angle_refined_deg1.782
r_mcangle_it1.756
r_mcbond_it0.9
r_chiral_restr0.126
r_bond_refined_d0.022
r_gen_planes_refined0.009
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_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 Atoms33736
Nucleic Acid Atoms
Solvent Atoms832
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing