3UUW

1.63 Angstrom Resolution Crystal Structure of Dehydrogenase (MviM) from Clostridium difficile.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TLT 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5295Protein solution: 0.3M Sodium chloride, 0.01M HEPES (pH 7.5), Screen solution: 0.2M Calcium chloride, 2% Glycerol, 20% PEG 3350, 0.01M NAD, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.3547.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.521α = 98.1
b = 69.535β = 106.97
c = 83.098γ = 115.73
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMirrors2011-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97855APS21-ID-D

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
11.633097.10.06516.74.3155282155282-322.3
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)
11.631.6694.80.5782.754.27631

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1TLT1.6329.97146631146631776397.060.159850.159850.158040.19457RANDOM18.689
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]
0.51.27-0.361.08-0.2-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.443
r_dihedral_angle_4_deg14.647
r_dihedral_angle_3_deg10.467
r_scangle_it4.775
r_dihedral_angle_1_deg4.33
r_scbond_it2.954
r_mcangle_it1.794
r_angle_refined_deg1.351
r_mcbond_it0.995
r_angle_other_deg0.835
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.443
r_dihedral_angle_4_deg14.647
r_dihedral_angle_3_deg10.467
r_scangle_it4.775
r_dihedral_angle_1_deg4.33
r_scbond_it2.954
r_mcangle_it1.794
r_angle_refined_deg1.351
r_mcbond_it0.995
r_angle_other_deg0.835
r_mcbond_other0.316
r_chiral_restr0.086
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9654
Nucleic Acid Atoms
Solvent Atoms1191
Heterogen Atoms91

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling