1Y7M

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.9294.1PEG 3350, acetate, lithium sulfate, cadmium chloride, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 294.1K, pH 4.90
Crystal Properties
Matthews coefficientSolvent content
2.448.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.276α = 90
b = 63.91β = 90
c = 93.679γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.3CCDADSC QUANTUM 42004-04-04MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X9B0.97946, 0.97919, 0.97178NSLSX9B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.053099.10.05715.52.2218052
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)
2.052.12990.4592.82.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT2.05302180520691111499.80.2140.2110.27RANDOM23.6
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]
4.23-1.75-2.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.449
r_scangle_it2.9
r_scbond_it1.872
r_angle_refined_deg1.441
r_mcangle_it0.968
r_angle_other_deg0.854
r_mcbond_it0.548
r_nbd_other0.237
r_symmetry_vdw_other0.225
r_nbd_refined0.206
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.449
r_scangle_it2.9
r_scbond_it1.872
r_angle_refined_deg1.441
r_mcangle_it0.968
r_angle_other_deg0.854
r_mcbond_it0.548
r_nbd_other0.237
r_symmetry_vdw_other0.225
r_nbd_refined0.206
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.189
r_symmetry_vdw_refined0.184
r_chiral_restr0.09
r_nbtor_other0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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 Atoms2468
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing