3LXD

Crystal Structure of Ferredoxin Reductase ArR from Novosphingobium aromaticivorans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q1RPDB ENTRY 1Q1R

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.62910.1M HEPES, 17% PEG 8000, 0.1M potassium phosphate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.9358.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.071α = 90
b = 140.071β = 90
c = 52.217γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVmirrors2008-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
12.55099.80.09221.17.11854218500-3
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)
12.52.5999.60.4553.66.61783

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1Q1R2.528.01175491749994899.710.191990.189210.2443RANDOM34.094
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]
-1.26-1.262.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.208
r_dihedral_angle_4_deg19.632
r_dihedral_angle_3_deg18.694
r_dihedral_angle_1_deg4.98
r_scangle_it1.437
r_angle_refined_deg1.125
r_scbond_it0.797
r_mcangle_it0.595
r_mcbond_it0.313
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.208
r_dihedral_angle_4_deg19.632
r_dihedral_angle_3_deg18.694
r_dihedral_angle_1_deg4.98
r_scangle_it1.437
r_angle_refined_deg1.125
r_scbond_it0.797
r_mcangle_it0.595
r_mcbond_it0.313
r_chiral_restr0.077
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3019
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms53

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling