7CUO | pdb_00007cuo

IclR transcription factor complexed with 4-hydroxybenzoic acid from Microbacterium hydrocarbonoxydans

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5H1A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES monohydrate, pH 6.5, 0.1 M sodium phosphate monobasic monohydrate, 0.1 M potassium phosphate monobasic and 2.0 M sodium chloride

Crystal Properties
Matthews coefficient	Solvent content
3	58.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.08	α = 90
b = 83.08	β = 90
c = 203.89	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 315r		2016-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	50	99.9	0.09	1	19.8	7.2		49164

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.848	0.87	2.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5h1a	2	44.484	49157	2407	99.927	0.203	0.2019	0.21	0.2179	0.22	29.131

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]
1.362			1.362		-2.725

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.91
r_dihedral_angle_4_deg	18.114
r_dihedral_angle_3_deg	14.477
r_dihedral_angle_1_deg	6.349
r_lrange_it	5.51
r_lrange_other	5.471
r_scangle_it	3.873
r_scangle_other	3.872
r_mcangle_it	2.654
r_mcangle_other	2.654
r_scbond_it	2.368
r_scbond_other	2.367
r_mcbond_it	1.678
r_mcbond_other	1.667
r_angle_refined_deg	1.363
r_angle_other_deg	1.326
r_symmetry_nbd_refined	0.213
r_nbd_refined	0.203
r_symmetry_nbd_other	0.186
r_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.147
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_other	0.118
r_symmetry_nbtor_other	0.078
r_xyhbond_nbd_other	0.077
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3659
Nucleic Acid Atoms
Solvent Atoms	210
Heterogen Atoms	60

Software

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