1PVO | pdb_00001pvo

X-ray crystal structure of Rho transcription termination factor in complex with ssRNA substrate and ANPPNP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PV4

Crystallization

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

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.249	α = 90
b = 204.649	β = 96.54
c = 147.788	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	2003-01-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.00	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3	50	95.7	0.04	0.05	15.3		77507	64912	2.5	2.5	92

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.12	95		0.274	0.332	2.5	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	1PV4	3	20	3	77507	70421	3727	95.7	0.27381	0.27084	0.24	0.30369	0.25	RANDOM	61.251

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]
0.57		-1.66	1.42		-2.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.096
r_scangle_it	2.579
r_scbond_it	1.43
r_angle_refined_deg	1.252
r_mcangle_it	1.098
r_mcbond_it	0.575
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.225
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.107

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.096
r_scangle_it	2.579
r_scbond_it	1.43
r_angle_refined_deg	1.252
r_mcangle_it	1.098
r_mcbond_it	0.575
r_nbd_refined	0.248
r_symmetry_vdw_refined	0.225
r_xyhbond_nbd_refined	0.165
r_chiral_restr	0.107
r_symmetry_hbond_refined	0.06
r_bond_refined_d	0.01
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18846
Nucleic Acid Atoms	200
Solvent Atoms	14
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	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.