5GNP

Crystal structure of a Z-ring associated protein from Salmonella typhimurium

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	Sodium malonate, HEPES, Jeffamin ED-2001(pH7.0).

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.239	α = 90
b = 84.239	β = 90
c = 149.865	γ = 120

Symmetry
Space Group	P 63 2 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	RAYONIX MX225HE		2016-04-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.000	SPring-8	BL38B1

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	2.6	50	99.7	0.16	48.6	13		8289

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	2.8	2.85	100		0.649	5.9

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	MOLECULAR REPLACEMENT	THROUGHOUT	2.8	50	7871	383	99.54	0.25283	0.25134	0.25	0.2829	0.28	RANDOM	82.374

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]
0.63	0.32		0.63		-2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.23
r_dihedral_angle_3_deg	15.119
r_dihedral_angle_4_deg	13.704
r_long_range_B_refined	7.774
r_long_range_B_other	7.769
r_dihedral_angle_1_deg	5.15
r_mcangle_it	4.864
r_mcangle_other	4.862
r_scangle_other	4.65
r_mcbond_it	2.85
r_mcbond_other	2.849
r_scbond_it	2.723
r_scbond_other	2.722
r_angle_refined_deg	0.927
r_angle_other_deg	0.707
r_chiral_restr	0.05
r_bond_refined_d	0.005
r_bond_other_d	0.005
r_gen_planes_refined	0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1983
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing