4LVC

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3N58PDB entry 3N58

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12920.2 M ammonium acetate, pH 7.1, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.3547.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.72α = 90
b = 176.47β = 90
c = 104.27γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225mirrors2011-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
11.7447.8598.70.08612.346.37203245200550-3
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)
11.741.79970.6941.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTR-FREEPDB entry 3N581.7447.8520324519953810111000.147750.147630.17222RANDOM21.592
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]
0.02-0.070.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.013
r_dihedral_angle_4_deg15.545
r_dihedral_angle_3_deg13.317
r_dihedral_angle_1_deg6.02
r_scangle_it4.115
r_scbond_it2.568
r_angle_refined_deg1.618
r_mcangle_it1.599
r_angle_other_deg0.961
r_mcbond_it0.907
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.013
r_dihedral_angle_4_deg15.545
r_dihedral_angle_3_deg13.317
r_dihedral_angle_1_deg6.02
r_scangle_it4.115
r_scbond_it2.568
r_angle_refined_deg1.618
r_mcangle_it1.599
r_angle_other_deg0.961
r_mcbond_it0.907
r_mcbond_other0.283
r_chiral_restr0.102
r_bond_refined_d0.018
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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_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 Atoms14468
Nucleic Acid Atoms
Solvent Atoms1704
Heterogen Atoms338

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
PHASERphasing