2V7U

X-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g mutant complexed with s-adenosylmethionine and chloride ion


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RQPPDB ENTRY 1RQP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.60.1M CITRATE-PHOSPHATE BUFFER PH4.6, 20%(W/V) PEG1000, 0.2M LICL
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.224α = 90
b = 129.377β = 90
c = 183.08γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEOSMIC MIRRORS2006-05-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
1230960.0817.84.9558673.3
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)
122.198.60.363.34.6

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 1RQP230.755867294495.80.1660.1640.204RANDOM23.17
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]
-0.520.270.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.312
r_dihedral_angle_4_deg16.097
r_dihedral_angle_3_deg13.122
r_dihedral_angle_1_deg6.82
r_scangle_it2.324
r_scbond_it1.541
r_angle_refined_deg1.352
r_mcangle_it0.902
r_mcbond_it0.591
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.312
r_dihedral_angle_4_deg16.097
r_dihedral_angle_3_deg13.122
r_dihedral_angle_1_deg6.82
r_scangle_it2.324
r_scbond_it1.541
r_angle_refined_deg1.352
r_mcangle_it0.902
r_mcbond_it0.591
r_nbtor_refined0.304
r_symmetry_vdw_refined0.222
r_nbd_refined0.19
r_symmetry_hbond_refined0.145
r_xyhbond_nbd_refined0.134
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.005
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_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 Atoms6654
Nucleic Acid Atoms
Solvent Atoms744
Heterogen Atoms84

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing