2WOC | pdb_00002woc

Crystal Structure of the dinitrogenase reductase-activating glycohydrolase (DRAG) from Rhodospirillum rubrum


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0238.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.771α = 80.84
b = 47.537β = 86.56
c = 95.212γ = 85.83
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDCCD2008-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.294.0789.80.11133.935220325.3
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)
12.22.3258.90.472.53.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.24033434178089.790.177570.174250.170.240160.24RANDOM25.495
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]
0.64-1.750.530.320.26-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.87
r_dihedral_angle_3_deg17.085
r_dihedral_angle_4_deg16.58
r_dihedral_angle_1_deg4.784
r_scangle_it1.855
r_scbond_it1.135
r_angle_refined_deg1.113
r_mcangle_it0.498
r_nbtor_refined0.293
r_mcbond_it0.267
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.87
r_dihedral_angle_3_deg17.085
r_dihedral_angle_4_deg16.58
r_dihedral_angle_1_deg4.784
r_scangle_it1.855
r_scbond_it1.135
r_angle_refined_deg1.113
r_mcangle_it0.498
r_nbtor_refined0.293
r_mcbond_it0.267
r_symmetry_vdw_refined0.255
r_symmetry_hbond_refined0.198
r_nbd_refined0.189
r_xyhbond_nbd_refined0.147
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.003
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 Atoms6612
Nucleic Acid Atoms
Solvent Atoms372
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing