2H2A | pdb_00002h2a

Crystal structure of Nicotinic acid mononucleotide adenylyltransferase from Staphylococcus aureus: product bound form 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2H29PDB ENTRY 2H29

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110mg/ml protein, 50mM Hepes pH 7.2, 300mM KCl, 0.5mM TCEP, 1mM EDTA mixed in equal volume of 20% PEG8000(w/v), 100mM MES pH 6.0, 0.2M Ca(OAc)2
Crystal Properties
Matthews coefficientSolvent content
2.9157.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.303α = 90
b = 83.649β = 90
c = 99.113γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray175IMAGE PLATERIGAKU RAXIS IV2005-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
123099.40.09925.36.1354011
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)
122.0794.60.5322.834.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2H292.13012235729357154499.90.2020.20.20.2390.24RANDOM28.76
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]
-1.060.170.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.41
r_dihedral_angle_4_deg21.942
r_dihedral_angle_3_deg16.013
r_dihedral_angle_1_deg6.005
r_scangle_it4.023
r_scbond_it2.759
r_mcangle_it2.039
r_angle_refined_deg1.746
r_mcbond_it1.301
r_symmetry_hbond_refined0.413
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.41
r_dihedral_angle_4_deg21.942
r_dihedral_angle_3_deg16.013
r_dihedral_angle_1_deg6.005
r_scangle_it4.023
r_scbond_it2.759
r_mcangle_it2.039
r_angle_refined_deg1.746
r_mcbond_it1.301
r_symmetry_hbond_refined0.413
r_nbtor_refined0.296
r_nbd_refined0.19
r_xyhbond_nbd_refined0.178
r_symmetry_vdw_refined0.152
r_chiral_restr0.143
r_bond_refined_d0.02
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_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 Atoms3116
Nucleic Acid Atoms
Solvent Atoms170
Heterogen Atoms95

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling