3Q20

Crystal structure of RbcX C103A mutant from Thermosynechococcus elongatus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52920.1M sodium acetate, 1.0M 1,6-hexanediol, 0.01M cobalt(II) chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.5151.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.78α = 90
b = 67.733β = 90
c = 94.544γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252008-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.741.296.20.04729.95.231245-331.9
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)
11.71.7671.80.432.22.9

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 REPLACEMENTR FREEPDB ENTRY 2PEQ1.7141.229886128095.80.18330.182030.21112RANDOM34.773
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]
1.33-0.46-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.927
r_dihedral_angle_4_deg19.474
r_dihedral_angle_3_deg14.255
r_dihedral_angle_1_deg5.13
r_scangle_it3.754
r_scbond_it2.289
r_angle_other_deg2.233
r_angle_refined_deg1.592
r_mcangle_it1.517
r_mcbond_it0.908
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.927
r_dihedral_angle_4_deg19.474
r_dihedral_angle_3_deg14.255
r_dihedral_angle_1_deg5.13
r_scangle_it3.754
r_scbond_it2.289
r_angle_other_deg2.233
r_angle_refined_deg1.592
r_mcangle_it1.517
r_mcbond_it0.908
r_mcbond_other0.296
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1797
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms24

Software

Software
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling