3KDO

Crystal structure of Type III Rubisco SP6 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, 90mM CaCl2, 5% PEG6000, 10% MPD, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1560.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.481α = 90
b = 246.573β = 104.73
c = 134.83γ = 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
12.365099.60.08213.1249468
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)
2.362.499.20.3892.5

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 1GEH2.3638.462367211253099.380.221110.218860.2638RANDOM31.605
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]
0.54-2.52-2.10.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.139
r_dihedral_angle_4_deg13.734
r_dihedral_angle_3_deg11.065
r_dihedral_angle_1_deg3.968
r_scangle_it0.685
r_angle_refined_deg0.589
r_scbond_it0.392
r_mcangle_it0.379
r_mcbond_it0.204
r_chiral_restr0.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.139
r_dihedral_angle_4_deg13.734
r_dihedral_angle_3_deg11.065
r_dihedral_angle_1_deg3.968
r_scangle_it0.685
r_angle_refined_deg0.589
r_scbond_it0.392
r_mcangle_it0.379
r_mcbond_it0.204
r_chiral_restr0.042
r_bond_refined_d0.002
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms34034
Nucleic Acid Atoms
Solvent Atoms1811
Heterogen Atoms220

Software

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