3JXD | pdb_00003jxd

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

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	Rubidium chloride, PEG 400, Tris-HCl, MgCl2, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.82	67.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.007	α = 90
b = 64.007	β = 90
c = 101.623	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	1.000	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	2.1	41.34	99.3	0.142	33.2	12.5	23743	23743

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)
	2.1	2.15	99.6		0.636	4.5	10.4	1762

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	2.1	41.34	1	22529	1214	99.3	0.183	0.18	0.17	0.225	0.22	RANDOM	26.546

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]
-0.04			-0.04		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.289
r_dihedral_angle_4_deg	14.438
r_dihedral_angle_3_deg	13.304
r_dihedral_angle_1_deg	5.476
r_scangle_it	4.247
r_scbond_it	2.909
r_angle_refined_deg	2.229
r_mcangle_it	1.956
r_mcbond_it	1.144
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.289
r_dihedral_angle_4_deg	14.438
r_dihedral_angle_3_deg	13.304
r_dihedral_angle_1_deg	5.476
r_scangle_it	4.247
r_scbond_it	2.909
r_angle_refined_deg	2.229
r_mcangle_it	1.956
r_mcbond_it	1.144
r_nbtor_refined	0.302
r_xyhbond_nbd_refined	0.195
r_nbd_refined	0.191
r_symmetry_hbond_refined	0.183
r_chiral_restr	0.129
r_symmetry_vdw_refined	0.125
r_bond_refined_d	0.02
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1030
Nucleic Acid Atoms	814
Solvent Atoms	288
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	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.