3C3K | pdb_00003c3k

Crystal structure of an uncharacterized protein from Actinobacillus succinogenes

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294	0.2 M Magnesium chloride, 0.1 M Bis-tris, 25% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.888	α = 90
b = 67.602	β = 90
c = 204.802	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	ADSC QUANTUM 315	Mirrors	2008-01-24	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	1.99	50	86.4	0.088	8.4	3		55962

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	1.99	2.06	38.4		0.245		1.8	2517

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	1.99	30.47	31315	1596	100	0.183	0.18	0.18	0.231	0.23	RANDOM	19.901

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]
0.02			-0.03		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.785
r_dihedral_angle_4_deg	17.973
r_dihedral_angle_3_deg	16.446
r_dihedral_angle_1_deg	6.395
r_scangle_it	4.661
r_scbond_it	3.251
r_angle_refined_deg	1.994
r_mcangle_it	1.886
r_mcbond_it	1.208
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.785
r_dihedral_angle_4_deg	17.973
r_dihedral_angle_3_deg	16.446
r_dihedral_angle_1_deg	6.395
r_scangle_it	4.661
r_scbond_it	3.251
r_angle_refined_deg	1.994
r_mcangle_it	1.886
r_mcbond_it	1.208
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.27
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.177
r_symmetry_hbond_refined	0.157
r_chiral_restr	0.156
r_bond_refined_d	0.022
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4120
Nucleic Acid Atoms
Solvent Atoms	253
Heterogen Atoms	13

Software

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