3KG4 | pdb_00003kg4

Crystal structure of an uncharacterized protein from Mannheimia succiniciproducens

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	294	100mM Bis-Tris pH 5.5, 22% PEG 3350, 200mM ammonium sulfate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.827	α = 90
b = 81.827	β = 90
c = 61.937	γ = 120

Symmetry
Space Group	P 63

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		2009-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	0.97958	APS	31-ID

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	1.95	70.864	99	0.086	0.086	25.7	23.1	17315	17142			26.7

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	1.95	2.06	98.4		0.33	0.33	10.2	23.2	2470

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 (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	1.95	20	17298	17123	869	98.99	0.212	0.211	0.21	0.242	0.24	RANDOM	36.145

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]
-0.12	-0.06		-0.12		0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.831
r_dihedral_angle_3_deg	15.57
r_dihedral_angle_4_deg	14.501
r_dihedral_angle_1_deg	6.839
r_scangle_it	4.129
r_scbond_it	2.591
r_mcangle_it	2.022
r_angle_refined_deg	1.501
r_mcbond_it	1.103
r_angle_other_deg	0.845

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1433
Nucleic Acid Atoms
Solvent Atoms	63
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

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.