3MS5 | pdb_00003ms5

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.2M Ammonium citrate, 20% PEG 3350, 6% diamine hexan, 10mM ZnSO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.366	α = 90
b = 107.366	β = 90
c = 205.054	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2009-10-24	M	SIRAS
2	1		CCD	MARMOSAIC 225 mm CCD		2010-02-04

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.0084	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.82	84.69	99.4	0.083	0.083	12.3	5.5		40755

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)	Redundancy	Number Unique Reflections (All)
	1.82	1.92	96.2		0.452	0.452	3.3	5.3	30263

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	1.82	19.45	38693	38693	2059	99.27	0.14856	0.14856	0.14671	0.15	0.18257	0.19	RANDOM	19.778

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]
1.11	0.56		1.11		-1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.123
r_dihedral_angle_4_deg	18.527
r_dihedral_angle_3_deg	12.76
r_dihedral_angle_1_deg	6.266
r_angle_refined_deg	1.6
r_angle_other_deg	0.962
r_chiral_restr	0.104
r_bond_refined_d	0.019
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	3101
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	58

Software

Software
Software Name	Purpose
MAR345	data collection
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling