3OOP | pdb_00003oop

The structure of a protein with unknown function from Listeria innocua Clip11262

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.2M calcium acetate, 0.1M tris pH7.0, 20%w/v PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.687	α = 90
b = 77.834	β = 113.36
c = 33.065	γ = 90

Symmetry
Space Group	C 1 2 1

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 315r	mirror	2010-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9792	APS	19-ID

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	1.78	50	96.2	0.082	49.37	4.3	13923	13923

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)
	1.78	1.81	81.3		0.271	6.56	3.7	599

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 (All)	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	1.78	47.21	13225	13225	694	96.37	0.21156	0.21156	0.21022	0.2104	0.23638	0.235	RANDOM	38.168

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]
0.47		2.02	0.5		0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.919
r_dihedral_angle_4_deg	18.097
r_dihedral_angle_3_deg	16.063
r_dihedral_angle_1_deg	4.171
r_scangle_it	4.161
r_scbond_it	2.47
r_mcangle_it	1.692
r_rigid_bond_restr	1.159
r_angle_refined_deg	1.026
r_mcbond_it	0.896

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.919
r_dihedral_angle_4_deg	18.097
r_dihedral_angle_3_deg	16.063
r_dihedral_angle_1_deg	4.171
r_scangle_it	4.161
r_scbond_it	2.47
r_mcangle_it	1.692
r_rigid_bond_restr	1.159
r_angle_refined_deg	1.026
r_mcbond_it	0.896
r_chiral_restr	0.072
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1121
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms

Software

Software
Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
ARP	model building
WARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.