4BGM | pdb_00004bgm

Three dimensional structure of human gamma-butyrobetaine hydroxylase in complex with 3-Carboxy-N-(2-fluoroethyl)-N,N-dimethylpropan-1- aminium chloride

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O2G	PDB ENTRY 3O2G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	294	20 % PEG 3350, 1.5 % 1.6-DIAMINOHEXANE, 200 MM AMMONIUM CITRATE PH 7.0, 10 MM ZNSO4, 8 MM N-OXALYLGLYCINE, 4 MM INHIBITOR, PROTEIN 6.5 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-7 DAYS

Crystal Properties
Matthews coefficient	Solvent content
2.5	52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.182	α = 90
b = 107.182	β = 90
c = 205.171	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	MARRESEARCH	MIRRORS	2011-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-3		MAX II	I911-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.4	45.27	99.2	0.1	9.4	3.3		17821			36.529

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	100		0.43	2.6	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3O2G	2.4	45.27	16864	906	98.41	0.16007	0.15647	0.1637	0.22811	0.2289	RANDOM	27.691

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]
0.07	0.07		0.07		-0.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.005
r_dihedral_angle_4_deg	17.002
r_dihedral_angle_3_deg	14.153
r_dihedral_angle_1_deg	6.089
r_angle_refined_deg	1.412
r_angle_other_deg	0.754
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms	Number
Protein Atoms	3119
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling