3MS5

Crystal Structure of Human gamma-butyrobetaine,2-oxoglutarate dioxygenase 1 (BBOX1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.2M Ammonium citrate, 20% PEG 3350, 6% diamine hexan, 10mM ZnSO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5351.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.366α = 90
b = 107.366β = 90
c = 205.054γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-10-24MSIRAS
21CCDMARMOSAIC 225 mm CCD2010-02-04
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I031.0084DiamondI03
2SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.8284.6999.40.0830.08312.35.540755
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.821.9296.20.4520.4523.35.330263

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRASTHROUGHOUT1.8219.453869338693205999.270.148560.148560.146710.18257RANDOM19.778
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]
1.110.561.11-1.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.123
r_dihedral_angle_4_deg18.527
r_dihedral_angle_3_deg12.76
r_dihedral_angle_1_deg6.266
r_angle_refined_deg1.6
r_angle_other_deg0.962
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.123
r_dihedral_angle_4_deg18.527
r_dihedral_angle_3_deg12.76
r_dihedral_angle_1_deg6.266
r_angle_refined_deg1.6
r_angle_other_deg0.962
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3101
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms58

Software

Software
Software NamePurpose
MAR345data collection
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling