4JC0 | pdb_00004jc0

Crystal structure of Thermotoga maritima holo RimO in complex with pentasulfide, Northeast Structural Genomics Consortium Target VR77

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	10	291	Protein solution: 10 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 20 mg/ml, 5 DTT, 10 equivalents FeCl3 and Na2S. Reservoir solution: 100 mM CAPS pH 10.0, 40% PEG 4000, 100 mM Sodium thiosulfate, MICROBATCH UNDER OIL, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.721	α = 90
b = 86.948	β = 90
c = 172.795	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	MAR CCD 165 mm	mirrors	2011-06-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.979	NSLS	X4C

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	3.3	41.45	92.4	0.136	0.091	13.71	4.9	63690	14135			85.6

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	3.42	81.4		0.407	0.368	2.34	4.1

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	2QGQ	3.3	41.46	14135	11747	1210	83.1	0.245	0.245	0.23	0.296	0.29	RANDOM	101.7

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]
-16.78			-32.01		48.79

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.1
c_angle_deg	1.1
c_improper_angle_d	0.69
c_bond_d	0.01
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6808
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	42

Software

Software
Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing