6ALM | pdb_00006alm

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)
Type	Source	Accession Code	Details
experimental model	PDB	2WBO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	1 M 2-oxoglutarate, 0.1 M Tris pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
1.84	33.25

Crystal Data

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

Symmetry
Space Group	C 1 2 1

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		2014-10-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	1.0	APS	21-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	50	97.4	0.053	0.057	0.02	8.1	7.7		40551

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)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	92.5		0.657	0.705	0.255	0.91		7.3

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	2WBO	1.6	50	38492	2050	97.27	0.1993	0.1977	0.21	0.2311	0.24	RANDOM	20.377

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	-0.09		0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.71
r_dihedral_angle_4_deg	13.046
r_dihedral_angle_3_deg	11.314
r_dihedral_angle_1_deg	5.208
r_angle_refined_deg	0.947
r_angle_other_deg	0.692
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.71
r_dihedral_angle_4_deg	13.046
r_dihedral_angle_3_deg	11.314
r_dihedral_angle_1_deg	5.208
r_angle_refined_deg	0.947
r_angle_other_deg	0.692
r_chiral_restr	0.052
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2647
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	23

Software

Software
Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.