3E10

Crystal structure of Putative NADH Oxidase (NP_348178.1) from CLOSTRIDIUM ACETOBUTYLICUM at 1.40 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720.0000% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties
Matthews coefficientSolvent content
2.2645.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.077α = 90
b = 83.528β = 90
c = 51.891γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing)2008-07-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.91837,0.97908,0.97849SSRLBL11-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.429.2731000.0960.0963.77099710.08
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.41.441000.5010.5011.53.65198

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 DIFFRACTIONMADTHROUGHOUT1.429.27370948358399.970.1320.130.168RANDOM9.24
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]
0.02-0.050.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.53
r_dihedral_angle_4_deg15.166
r_dihedral_angle_3_deg11.942
r_sphericity_free6.841
r_dihedral_angle_1_deg6.22
r_scangle_it5.868
r_scbond_it4.363
r_sphericity_bonded3.706
r_mcangle_it3.06
r_mcbond_it2.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.53
r_dihedral_angle_4_deg15.166
r_dihedral_angle_3_deg11.942
r_sphericity_free6.841
r_dihedral_angle_1_deg6.22
r_scangle_it5.868
r_scbond_it4.363
r_sphericity_bonded3.706
r_mcangle_it3.06
r_mcbond_it2.49
r_rigid_bond_restr1.773
r_angle_refined_deg1.569
r_mcbond_other1.428
r_angle_other_deg1.012
r_nbd_refined0.224
r_symmetry_vdw_other0.224
r_nbd_other0.208
r_nbtor_refined0.182
r_xyhbond_nbd_refined0.179
r_symmetry_hbond_refined0.162
r_symmetry_vdw_refined0.16
r_chiral_restr0.093
r_nbtor_other0.088
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2860
Nucleic Acid Atoms
Solvent Atoms519
Heterogen Atoms134

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing