4QIC | pdb_00004qic

Co-Crystal Structure of Anti-anti-sigma factor PhyR complexed with Anti-sigma factor NepR from Bartonella quintana

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4G97	PDB ENTRY 4G97

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	Morpheus(c8): 12.5% PEG-1000, 12.5% PEG-3350, 12.5% MPD, 0.1M MOPS/ HEPES-Na, 0.03M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.8	α = 90
b = 86.7	β = 90
c = 106.11	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	Beryllium Lenses	2004-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97857	APS	21-ID-F

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	2.05	50	99.9	0.075	16.64	6.2	45212	45189		-3	34.274

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	2.05	2.1	100		0.532	3.31

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	PDB ENTRY 4G97	2.05	19.91	47309	45074	2235	99.83	0.1905	0.1891	0.1957	0.2186	0.2241	RANDOM	32.407

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]
-0.7			-0.79		1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.45
r_dihedral_angle_4_deg	20.346
r_dihedral_angle_3_deg	13.153
r_dihedral_angle_1_deg	5.517
r_mcangle_it	2.401
r_angle_refined_deg	1.432
r_mcbond_other	1.388
r_mcbond_it	1.387
r_angle_other_deg	0.809
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.45
r_dihedral_angle_4_deg	20.346
r_dihedral_angle_3_deg	13.153
r_dihedral_angle_1_deg	5.517
r_mcangle_it	2.401
r_angle_refined_deg	1.432
r_mcbond_other	1.388
r_mcbond_it	1.387
r_angle_other_deg	0.809
r_chiral_restr	0.081
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4508
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

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.