4MQD | pdb_00004mqd

Crystal structure of ComJ, inhibitor of the DNA degrading activity of NucA, from Bacillus subtilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	297	0.1M sodium acetate pH 4.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.73	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 125.826	α = 90
b = 125.826	β = 90
c = 37.013	γ = 120

Symmetry
Space Group	P 32

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		2013-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929	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	2.15	50	99.7	0.111	12.3	4.6	35143	35026		-3

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	2.15	2.19	99.9		0.974	1.54	4.1	1786

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	2.16	41.22	29654	29654	1514	83.79	0.1811	0.1811	0.1779	0.189	0.2404	0.2487	RANDOM	36.687

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]
-0.2	-0.2		-0.2		0.66

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.955
r_dihedral_angle_2_deg	28.334
r_sphericity_bonded	12.711
r_dihedral_angle_3_deg	10.806
r_dihedral_angle_4_deg	9.303
r_dihedral_angle_1_deg	5.213
r_angle_refined_deg	0.845
r_angle_other_deg	0.571
r_rigid_bond_restr	0.497
r_chiral_restr	0.055

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	32.955
r_dihedral_angle_2_deg	28.334
r_sphericity_bonded	12.711
r_dihedral_angle_3_deg	10.806
r_dihedral_angle_4_deg	9.303
r_dihedral_angle_1_deg	5.213
r_angle_refined_deg	0.845
r_angle_other_deg	0.571
r_rigid_bond_restr	0.497
r_chiral_restr	0.055
r_bond_refined_d	0.003
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4234
Nucleic Acid Atoms
Solvent Atoms	269
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
ARP/wARP	model building
RESOLVE	phasing
Coot	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.