4WNR

Structure of methanosarcina barkeri Roco2 RocCORdC bound to GDP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293.15Tris, Sodiumsulfate, Lithiumsulfate, PEG 400
Crystal Properties
Matthews coefficientSolvent content
4.7574.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.36α = 90
b = 109.36β = 90
c = 223.1γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.06997SLSX10SA

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
12.94999.60.07321.8481816918092
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)
12.93.0898.60.7952.848.1

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 REPLACEMENTTHROUGHOUT3DPU2.948.061727291099.70.241690.240290.26867RANDOM83.25
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]
-0.61-0.61-0.611.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.083
r_dihedral_angle_3_deg12.513
r_dihedral_angle_4_deg7.235
r_dihedral_angle_1_deg4.427
r_angle_refined_deg0.769
r_angle_other_deg0.658
r_chiral_restr0.046
r_bond_other_d0.005
r_bond_refined_d0.004
r_gen_planes_refined0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.083
r_dihedral_angle_3_deg12.513
r_dihedral_angle_4_deg7.235
r_dihedral_angle_1_deg4.427
r_angle_refined_deg0.769
r_angle_other_deg0.658
r_chiral_restr0.046
r_bond_other_d0.005
r_bond_refined_d0.004
r_gen_planes_refined0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms2621
Nucleic Acid Atoms
Solvent Atoms19
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing