2V6A

Crystal structure of Chlamydomonas reinhardtii Rubisco with large- subunit mutations V331A, G344S


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
2.1742.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.906α = 90
b = 196.629β = 90
c = 201.95γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-3ESRFID14-3

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
11.530960.082031.2781039
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)
11.51.5489.90.521.9

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 1GK81.5307407353924495.70.1770.1760.192RANDOM19.23
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]
0.340.49-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.136
r_dihedral_angle_4_deg15.45
r_dihedral_angle_3_deg13.021
r_dihedral_angle_1_deg5.963
r_scangle_it2.801
r_scbond_it1.832
r_angle_refined_deg1.286
r_mcangle_it1.122
r_mcbond_it0.719
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.136
r_dihedral_angle_4_deg15.45
r_dihedral_angle_3_deg13.021
r_dihedral_angle_1_deg5.963
r_scangle_it2.801
r_scbond_it1.832
r_angle_refined_deg1.286
r_mcangle_it1.122
r_mcbond_it0.719
r_nbtor_refined0.309
r_symmetry_vdw_refined0.214
r_nbd_refined0.199
r_symmetry_hbond_refined0.171
r_xyhbond_nbd_refined0.108
r_chiral_restr0.088
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms38207
Nucleic Acid Atoms
Solvent Atoms3492
Heterogen Atoms412

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing