3SNY

Crystal structure of a mutant T82R of a betagamma-crystallin domain from Clostridium beijerinckii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I9H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP27725-30% PEG 3350, 0.1M HEPES, 0.1-0.2M lithium sulphate, pH 7.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.754.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.314α = 90
b = 77.314β = 90
c = 77.738γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS IVVariMax optics2010-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
11.85500.02984.113.310242
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)
11.851.920.08131.812.7

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 REPLACEMENTTHROUGHOUT3I9H1.8550974749598.830.187810.18630.21981RANDOM17.046
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]
-0.27-0.270.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.61
r_dihedral_angle_3_deg10.179
r_dihedral_angle_1_deg5.154
r_dihedral_angle_4_deg2.679
r_scangle_it1.573
r_scbond_it0.932
r_angle_refined_deg0.871
r_mcangle_it0.659
r_mcbond_it0.344
r_chiral_restr0.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.61
r_dihedral_angle_3_deg10.179
r_dihedral_angle_1_deg5.154
r_dihedral_angle_4_deg2.679
r_scangle_it1.573
r_scbond_it0.932
r_angle_refined_deg0.871
r_mcangle_it0.659
r_mcbond_it0.344
r_chiral_restr0.056
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms689
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms11

Software

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