1PV4 | pdb_00001pv4

X-ray crystal structure of the Rho transcription termination factor in complex with single stranded DNA

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	0.05M Nacacodylate (pH 6.5), 0.05M NaCl, 2.5% PEG 8K, 20% glycerol, 0.3mM n-Nonyl-beta-D-thiomaltoside, 1mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 18K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.556	α = 90
b = 204.327	β = 95.86
c = 147.37	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	95	CCD	ADSC QUANTUM 4	mirrors	2002-02-10	M	MAD
2	1	x-ray		M	SAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.05, 1.0, 0.9794	ALS	8.3.1

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	3	50	96.1	0.046	15.5	2.2	74391	63958	3	3	89.4

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)
1,2	3	3.12	98.5		0.272	3.5	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SIR, MAD	THROUGHOUT	3	20	77075	63958	3379	97.9	0.27132	0.27132	0.26997	0.2444	0.29633	0.2684	RANDOM	62.668

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]
-1.14		-2.27	2.01		-1.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.735
r_scangle_it	3.767
r_scbond_it	2.16
r_mcangle_it	1.533
r_angle_refined_deg	1.467
r_mcbond_it	0.796
r_symmetry_vdw_refined	0.343
r_nbd_refined	0.311
r_symmetry_hbond_refined	0.27
r_xyhbond_nbd_refined	0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.735
r_scangle_it	3.767
r_scbond_it	2.16
r_mcangle_it	1.533
r_angle_refined_deg	1.467
r_mcbond_it	0.796
r_symmetry_vdw_refined	0.343
r_nbd_refined	0.311
r_symmetry_hbond_refined	0.27
r_xyhbond_nbd_refined	0.21
r_chiral_restr	0.103
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18846
Nucleic Acid Atoms	190
Solvent Atoms	41
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing
MLPHARE	phasing
SHARP	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.