5HYM

3-Hydroxybenzoate 6-hydroxylase from Rhodococcus jostii in complex with phosphatidylinositol

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4BJZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	30% PEG 4000, 0.2 M lithium sulphate, 0.1 M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.98	α = 90
b = 106.98	β = 90
c = 143.39	γ = 90

Symmetry
Space Group	I 41 2 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	ADSC QUANTUM 315		2011-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9763	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.3	43.64	99.7	0.16	0.172	0.061	0.992	8.4	7.5		18766

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	2.3	2.38	100		0.547		5.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4BJZ	2.3	43.64	17415	1337	99.53	0.21	0.2059	0.2617	RANDOM	33.408

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]
-0.35			-0.35		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.94
r_dihedral_angle_4_deg	15.175
r_dihedral_angle_3_deg	14.121
r_dihedral_angle_1_deg	6.944
r_mcangle_it	3.818
r_mcbond_it	2.444
r_mcbond_other	2.444
r_angle_refined_deg	1.753
r_angle_other_deg	1.025
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.94
r_dihedral_angle_4_deg	15.175
r_dihedral_angle_3_deg	14.121
r_dihedral_angle_1_deg	6.944
r_mcangle_it	3.818
r_mcbond_it	2.444
r_mcbond_other	2.444
r_angle_refined_deg	1.753
r_angle_other_deg	1.025
r_chiral_restr	0.097
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3078
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	106

Software

Software
Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.