2WOE | pdb_00002woe

Crystal Structure of the D97N variant of dinitrogenase reductase- activating glycohydrolase (DRAG) from Rhodospirillum rubrum in complex with ADP-ribose


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.11α = 90
b = 84.36β = 90
c = 146.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2008-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.973.1397.80.112.34.478445322.4
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)
11.9298.60.512.74.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNONE1.93074423395597.250.169120.16710.170.207310.21RANDOM22.657
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]
1.86-2.050.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.936
r_dihedral_angle_4_deg17.142
r_dihedral_angle_3_deg14.261
r_dihedral_angle_1_deg5.153
r_scangle_it2.132
r_scbond_it1.397
r_angle_refined_deg1.198
r_angle_other_deg0.919
r_mcangle_it0.653
r_mcbond_it0.594
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.936
r_dihedral_angle_4_deg17.142
r_dihedral_angle_3_deg14.261
r_dihedral_angle_1_deg5.153
r_scangle_it2.132
r_scbond_it1.397
r_angle_refined_deg1.198
r_angle_other_deg0.919
r_mcangle_it0.653
r_mcbond_it0.594
r_symmetry_vdw_other0.241
r_nbd_refined0.202
r_nbd_other0.182
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.162
r_symmetry_vdw_refined0.158
r_mcbond_other0.124
r_symmetry_hbond_refined0.108
r_nbtor_other0.084
r_chiral_restr0.065
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms6612
Nucleic Acid Atoms
Solvent Atoms758
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing