3QVO

Structure of a Rossmann-fold NAD(P)-binding family protein from Shigella flexneri.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.92941M potassium/sodium phosphate pH 6.9, 1.25mM DNTB, 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.3463.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.524α = 90
b = 73.524β = 90
c = 130.246γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-04-06MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97953, 0.97940APS19-ID

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
12.35099.50.0828.911.61645516455-3
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)
12.32.341000.64510.7

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 DIFFRACTIONMADTHROUGHOUT2.336.76155841558483199.440.216520.214810.25075RANDOM56.042
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]
2.632.63-5.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.747
r_dihedral_angle_4_deg15.397
r_dihedral_angle_3_deg14.586
r_dihedral_angle_1_deg7.182
r_scangle_it4.469
r_scbond_it2.702
r_angle_refined_deg1.621
r_mcangle_it1.544
r_angle_other_deg0.884
r_mcbond_it0.814
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.747
r_dihedral_angle_4_deg15.397
r_dihedral_angle_3_deg14.586
r_dihedral_angle_1_deg7.182
r_scangle_it4.469
r_scbond_it2.702
r_angle_refined_deg1.621
r_mcangle_it1.544
r_angle_other_deg0.884
r_mcbond_it0.814
r_mcbond_other0.189
r_chiral_restr0.095
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms1508
Nucleic Acid Atoms
Solvent Atoms75
Heterogen Atoms13

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building