2NLO

Crystal Structure of the Quinate Dehydrogenase from Corynebacterium glutamicum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NVTPDB ENTRY 1NVT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.0840.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.784α = 90
b = 63.021β = 92.24
c = 35.527γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7B0.843EMBL/DESY, HAMBURGBW7B

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
11.67.9929404

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1NVT1.6437.9929404152697.640.1490.148120.16543RANDOM14.399
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]
0.18-0.04-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.942
r_dihedral_angle_4_deg19.444
r_dihedral_angle_3_deg11.536
r_dihedral_angle_1_deg5.709
r_scangle_it4.162
r_scbond_it3.022
r_mcangle_it2.626
r_mcbond_it2.391
r_angle_refined_deg1.135
r_angle_other_deg0.845
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.942
r_dihedral_angle_4_deg19.444
r_dihedral_angle_3_deg11.536
r_dihedral_angle_1_deg5.709
r_scangle_it4.162
r_scbond_it3.022
r_mcangle_it2.626
r_mcbond_it2.391
r_angle_refined_deg1.135
r_angle_other_deg0.845
r_mcbond_other0.596
r_symmetry_vdw_other0.335
r_nbd_refined0.21
r_symmetry_hbond_refined0.199
r_nbd_other0.195
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.145
r_symmetry_vdw_refined0.094
r_nbtor_other0.085
r_chiral_restr0.061
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2067
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing