2XR7

Crystal Structure of Nicotiana tabacum malonyltransferase (NtMat1) complexed with malonyl-coa


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.3M AMMONIUM ACETATE, 7% PEG 8K, 10% MPD, PH 5.5
Crystal Properties
Matthews coefficientSolvent content
3.564

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.079α = 90
b = 98.079β = 90
c = 151.84γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
21x-ray100CCDSX-1652005-10-25M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A
2SYNCHROTRONNSLS BEAMLINE X3ANSLSX3A

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
13.12099.40.11204256282
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)
13.13.2195.40.61.72.9

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 DIFFRACTIONSADTHROUGHOUTNONE3.12012928100199.60.230.2260.289RANDOM82.65
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]
0.680.68-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.572
r_dihedral_angle_4_deg20.852
r_dihedral_angle_3_deg20.305
r_dihedral_angle_1_deg7.765
r_scangle_it3.991
r_scbond_it2.358
r_angle_refined_deg1.503
r_mcangle_it0.815
r_mcbond_it0.37
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.572
r_dihedral_angle_4_deg20.852
r_dihedral_angle_3_deg20.305
r_dihedral_angle_1_deg7.765
r_scangle_it3.991
r_scbond_it2.358
r_angle_refined_deg1.503
r_mcangle_it0.815
r_mcbond_it0.37
r_chiral_restr0.107
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3544
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
Auto-Rickshawphasing