3HRL

Crystal structure of a putative endonuclease-like protein (ngo0050) from neisseria gonorrhoeae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	294	3M NaCl, 0.1M HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.39	63.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.922	α = 90
b = 52.922	β = 90
c = 102.295	γ = 120

Symmetry
Space Group	P 32 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		MIRROR	2009-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

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	22.33	99.9	0.07	0.07	21.712	5.8	23330	23330		-3

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	1.98	98.7		0.353	0.353	5.2	5.8

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	1.95	22.33	12588	11984	604	99.83	0.18521	0.18316	0.226	RANDOM	19.925

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]
1.65	0.82		1.65		-2.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.8
r_dihedral_angle_4_deg	12.846
r_dihedral_angle_3_deg	12.223
r_scangle_it	5.93
r_dihedral_angle_1_deg	5.733
r_scbond_it	3.529
r_mcangle_it	1.997
r_angle_refined_deg	1.615
r_mcbond_it	1.087
r_angle_other_deg	0.901
r_mcbond_other	0.314
r_chiral_restr	0.098
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	775
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	1

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing