2P2U

Crystal structure of putative host-nuclease inhibitor protein Gam from Desulfovibrio vulgaris

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	9	294	100mM Tris-HCl pH 9.0, 21% PEG 4000, 200mM Sodium acetate, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.62	66.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.03	α = 90
b = 93.408	β = 90
c = 104.166	γ = 90

Symmetry
Space Group	P 21 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	MAR CCD 165 mm		2007-02-24	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	2.75	19.976	98.5	0.143	0.143	12.3	7.4	15027	15027			72

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	2.75	2.9	98.2		0.475	0.475	3.3	7.6	2139

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.75	12	14847	14847	767	98.51	0.245	0.242	0.29	RANDOM	61.793

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]
2.15			-2.51		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.93
r_dihedral_angle_3_deg	23.476
r_dihedral_angle_4_deg	23.448
r_dihedral_angle_1_deg	7.64
r_scangle_it	5.318
r_scbond_it	3.363
r_angle_refined_deg	2.197
r_mcangle_it	2.001
r_mcbond_it	1.446
r_nbtor_refined	0.327

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.93
r_dihedral_angle_3_deg	23.476
r_dihedral_angle_4_deg	23.448
r_dihedral_angle_1_deg	7.64
r_scangle_it	5.318
r_scbond_it	3.363
r_angle_refined_deg	2.197
r_mcangle_it	2.001
r_mcbond_it	1.446
r_nbtor_refined	0.327
r_nbd_refined	0.268
r_symmetry_vdw_refined	0.248
r_xyhbond_nbd_refined	0.237
r_symmetry_hbond_refined	0.195
r_chiral_restr	0.144
r_bond_refined_d	0.024
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2377
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
SHELXD	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.