6ALM

VioC L-arginine hydroxylase bound to Fe(II), L-arginine, and 2-OXO-GLUTARIC ACID


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WBO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981 M 2-oxoglutarate, 0.1 M Tris pH 8.5
Crystal Properties
Matthews coefficientSolvent content
1.8433.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.336α = 90
b = 66.99β = 108.81
c = 62.665γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2014-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F1.0APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.65097.40.0530.0570.028.17.740551
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6392.50.6570.7050.2550.917.3

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 REPLACEMENTTHROUGHOUT2WBO1.65038492205097.270.19930.19770.2311RANDOM20.377
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]
1.15-2.09-0.090.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.71
r_dihedral_angle_4_deg13.046
r_dihedral_angle_3_deg11.314
r_dihedral_angle_1_deg5.208
r_angle_refined_deg0.947
r_angle_other_deg0.692
r_chiral_restr0.052
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.71
r_dihedral_angle_4_deg13.046
r_dihedral_angle_3_deg11.314
r_dihedral_angle_1_deg5.208
r_angle_refined_deg0.947
r_angle_other_deg0.692
r_chiral_restr0.052
r_bond_refined_d0.004
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2647
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms23

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing