3JU2

CRYSTAL STRUCTURE OF PROTEIN SMc04130 FROM Sinorhizobium meliloti 1021


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.22940.1M PHOSPHATE-CITRATE, PH 4.2, 20% PEG8000, 200MM SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
3.1661.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.102α = 90
b = 92.102β = 90
c = 157.345γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDADSC QUANTUM 315MIRRORS2009-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
11.8401000.071612.537235-5
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)
11.81.861000.950.511.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.82034816111596.680.200630.199190.24638RANDOM42.244
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]
0.190.10.19-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.952
r_dihedral_angle_4_deg15.495
r_dihedral_angle_3_deg14.309
r_dihedral_angle_1_deg9.322
r_scangle_it7.902
r_scbond_it5.479
r_mcangle_it4.643
r_mcbond_it3.764
r_angle_refined_deg1.476
r_nbtor_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.952
r_dihedral_angle_4_deg15.495
r_dihedral_angle_3_deg14.309
r_dihedral_angle_1_deg9.322
r_scangle_it7.902
r_scbond_it5.479
r_mcangle_it4.643
r_mcbond_it3.764
r_angle_refined_deg1.476
r_nbtor_refined0.293
r_nbd_refined0.162
r_symmetry_hbond_refined0.152
r_xyhbond_nbd_refined0.145
r_symmetry_vdw_refined0.138
r_chiral_restr0.097
r_metal_ion_refined0.037
r_bond_refined_d0.012
r_gen_planes_refined0.007
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2056
Nucleic Acid Atoms
Solvent Atoms192
Heterogen Atoms19

Software

Software
Software NamePurpose
SHELXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing