3A14

Crystal structure of DXR from Thermotoga maritima, in complex with NADPH


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52930.1M HEPES 40% MPD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5852.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.527α = 90
b = 108.527β = 90
c = 74.178γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 3152007-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

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
1276.759121
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.07100

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT276.7548232928980.2090.2080.236RANDOM38.61
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]
-0.52-0.521.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.016
r_dihedral_angle_4_deg17.782
r_dihedral_angle_3_deg14.627
r_dihedral_angle_1_deg5.633
r_scangle_it3.908
r_scbond_it2.435
r_mcangle_it1.497
r_angle_refined_deg1.397
r_mcbond_it0.921
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.016
r_dihedral_angle_4_deg17.782
r_dihedral_angle_3_deg14.627
r_dihedral_angle_1_deg5.633
r_scangle_it3.908
r_scbond_it2.435
r_mcangle_it1.497
r_angle_refined_deg1.397
r_mcbond_it0.921
r_nbtor_refined0.305
r_symmetry_vdw_refined0.242
r_xyhbond_nbd_refined0.157
r_chiral_restr0.091
r_symmetry_hbond_refined0.083
r_xyhbond_nbd_other0.079
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_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 Atoms5750
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms141

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing