2RG4 | pdb_00002rg4

Crystal structure of the uncharacterized protein Q2CBJ1_9RHOB from Oceanicola granulosus HTCC2516

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	0.1M Bis-tris, 0.3M Magnesium formate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.476	α = 90
b = 69.476	β = 90
c = 164.66	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC QUANTUM 315		2007-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97900	NSLS	X29A

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	1.8	50	98.7	0.076	9	6.2		70428

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	1.8	1.86	98.9		0.668		5.6	7041

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	SAD	THROUGHOUT	1.9	19.38	31410	1584	96.25	0.211	0.207	0.21	0.277	0.28	RANDOM	28.777

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.798
r_dihedral_angle_4_deg	19.183
r_dihedral_angle_3_deg	18.959
r_scbond_it	12.577
r_dihedral_angle_1_deg	12.014
r_scangle_it	6.55
r_mcangle_it	6.086
r_angle_refined_deg	2.343
r_mcbond_it	2.142
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.798
r_dihedral_angle_4_deg	19.183
r_dihedral_angle_3_deg	18.959
r_scbond_it	12.577
r_dihedral_angle_1_deg	12.014
r_scangle_it	6.55
r_mcangle_it	6.086
r_angle_refined_deg	2.343
r_mcbond_it	2.142
r_nbtor_refined	0.32
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.227
r_xyhbond_nbd_refined	0.208
r_symmetry_hbond_refined	0.195
r_chiral_restr	0.173
r_bond_refined_d	0.023
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3260
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	2

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
SHELXD	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.