4I76 | pdb_00004i76

Crystal structure of transcriptional regulator TM1030 with octanol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ID6	PDB ENTRY 2ID6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	30%w/v PEG 2K MME, 0.1M KSCN, 6%v/v octanol, pH 7.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.911	α = 90
b = 50.429	β = 129.15
c = 88.098	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	IMAGE PLATE	MAR scanner 300 mm plate			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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	2.1	50	95.5	0.12	7.3	4.5		23321

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	2.1	2.18	73.5		0.378		3.3	1768

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 2ID6	2.1	26.99	23318	1200	95.4	0.1963	0.1931	0.1983	0.2562	0.256	RANDOM	30.2997

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]
0.95		-0.14	0.14		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.71
r_dihedral_angle_3_deg	16.718
r_dihedral_angle_4_deg	15.946
r_dihedral_angle_1_deg	5.536
r_angle_refined_deg	1.637
r_angle_other_deg	1.172
r_chiral_restr	0.101
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3293
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	30

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing