3JXC | pdb_00003jxc

Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R1J	PDB entry 2R1J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	277	PEG 400, Thallium acetate, Tris-HCl, Magnesium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.249	α = 90
b = 64.249	β = 90
c = 100.82	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARMOSAIC 225 mm CCD		2008-03-05		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	0.97784	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.9	30.61	98.5	0.073	44.3	13.4	31737	31737

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	1.95	97.7		0.487	9.29	11.3	1591

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 2R1J	1.9	30.61	1	30146	1591	98.54	0.185	0.184	0.18	0.208	0.21	RANDOM	25.067

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.494
r_dihedral_angle_3_deg	12.307
r_dihedral_angle_4_deg	8.036
r_dihedral_angle_1_deg	4.085
r_scangle_it	3.22
r_scbond_it	2.122
r_angle_refined_deg	1.681
r_mcangle_it	1.468
r_mcbond_it	0.932
r_nbtor_refined	0.294

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.494
r_dihedral_angle_3_deg	12.307
r_dihedral_angle_4_deg	8.036
r_dihedral_angle_1_deg	4.085
r_scangle_it	3.22
r_scbond_it	2.122
r_angle_refined_deg	1.681
r_mcangle_it	1.468
r_mcbond_it	0.932
r_nbtor_refined	0.294
r_nbd_refined	0.191
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.11
r_symmetry_vdw_refined	0.106
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1030
Nucleic Acid Atoms	814
Solvent Atoms	279
Heterogen Atoms	4

Software

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