3PIL

Crystal structure of Mxr1 from Saccharomyces cerevisiae in reduced form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.62890.2M ammonium acetate, 0.1M sodium acetate, 30% polyethylene glycol 4,000, pH 4.6, VAPOR DIFFUSION, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.9837.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.31α = 90
b = 70.14β = 90
c = 74.03γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2008-12-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.0329.1798.421889
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.032.1489.6

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 REPLACEMENTTHROUGHOUT3BQE2.0429.1720726111799.730.208580.20660.24665RANDOM17.236
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]
-0.130.79-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.766
r_dihedral_angle_3_deg11.716
r_dihedral_angle_4_deg9.393
r_dihedral_angle_1_deg4.403
r_angle_refined_deg0.828
r_scangle_it0.495
r_scbond_it0.28
r_mcangle_it0.214
r_mcbond_it0.11
r_chiral_restr0.061
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.766
r_dihedral_angle_3_deg11.716
r_dihedral_angle_4_deg9.393
r_dihedral_angle_1_deg4.403
r_angle_refined_deg0.828
r_scangle_it0.495
r_scbond_it0.28
r_mcangle_it0.214
r_mcbond_it0.11
r_chiral_restr0.061
r_bond_refined_d0.006
r_gen_planes_refined0.002
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 Atoms2942
Nucleic Acid Atoms
Solvent Atoms342
Heterogen Atoms8

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling