3KDN

Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GEHPDB ENTRY 1GEH

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1M Acetate, 80mM CaCl2, 6% PEG6000, 10% MPD, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1160.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.474α = 90
b = 246.241β = 104.1
c = 133.08γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2009-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.095096.50.07115.4345208
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.092.1370.30.3842.3

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 1GEH2.0942.863277011738896.480.214630.212610.25286RANDOM26.249
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]
1.07-2.43-1.66-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.021
r_dihedral_angle_4_deg17.064
r_dihedral_angle_3_deg12.054
r_dihedral_angle_1_deg4.696
r_scangle_it1.344
r_scbond_it0.786
r_angle_refined_deg0.768
r_mcangle_it0.562
r_mcbond_it0.294
r_chiral_restr0.053
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.021
r_dihedral_angle_4_deg17.064
r_dihedral_angle_3_deg12.054
r_dihedral_angle_1_deg4.696
r_scangle_it1.344
r_scbond_it0.786
r_angle_refined_deg0.768
r_mcangle_it0.562
r_mcbond_it0.294
r_chiral_restr0.053
r_bond_refined_d0.004
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms34127
Nucleic Acid Atoms
Solvent Atoms2652
Heterogen Atoms220

Software

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