2V69

Crystal structure of Chlamydomonas reinhardtii Rubisco with a large- subunit mutation D473E


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GK8PDB ENTRY 1GK8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4449.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.242α = 90
b = 169.14β = 96.24
c = 137.179γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2004-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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
12.82098.40.0911.97.9125065
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)
12.82.998.60.63

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 1GK82.820118598622898.40.1980.1970.228RANDOM59.6
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]
5.18-2.01-2.54-3.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.096
r_dihedral_angle_3_deg16.682
r_dihedral_angle_4_deg15.392
r_dihedral_angle_1_deg6.305
r_scangle_it2.044
r_angle_refined_deg1.356
r_scbond_it1.24
r_mcangle_it1.08
r_mcbond_it0.612
r_symmetry_vdw_refined0.422
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.096
r_dihedral_angle_3_deg16.682
r_dihedral_angle_4_deg15.392
r_dihedral_angle_1_deg6.305
r_scangle_it2.044
r_angle_refined_deg1.356
r_scbond_it1.24
r_mcangle_it1.08
r_mcbond_it0.612
r_symmetry_vdw_refined0.422
r_symmetry_hbond_refined0.335
r_nbtor_refined0.314
r_nbd_refined0.213
r_xyhbond_nbd_refined0.143
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms37837
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms272

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing