2IU6 | pdb_00002iu6

REGULATION OF THE DHA OPERON OF LACTOCOCCUS LACTIS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OI2	PDB ENTRY 1OI2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		0.15 M DL-MALIC ACID PH 7.0, 20% PEG-3350

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.09	α = 90
b = 101.09	β = 90
c = 148.6	γ = 120

Symmetry
Space Group	P 32 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	110	IMAGE PLATE	RIGAKU RAXIS-IV			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300

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	40	100	0.08	22.6	12.38		59910		3

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	2.04	100		0.45	6.88	10.95

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 1OI2	2	30	58399	1497	100	0.173	0.173	0.17	0.198	0.2	RANDOM	30.98

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]
-1.08	-0.54		-1.08		1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.275
r_dihedral_angle_4_deg	27.749
r_dihedral_angle_3_deg	16.318
r_dihedral_angle_1_deg	6.863
r_scangle_it	3.938
r_scbond_it	2.682
r_mcangle_it	1.823
r_angle_refined_deg	1.662
r_mcbond_it	1.454
r_nbtor_refined	0.322
r_chiral_restr	0.29
r_nbd_refined	0.229
r_xyhbond_nbd_refined	0.168
r_symmetry_hbond_refined	0.149
r_symmetry_vdw_refined	0.148
r_bond_refined_d	0.013
r_gen_planes_refined	0.001
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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	4981
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing