3SN9 | pdb_00003sn9

Fic protein from NEISSERIA MENINGITIDIS mutant S182A/E186A in complex with AMPPNP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G03	PDB entry 2g03

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	21% PEG3350, 0.2 M di-ammonium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.313	α = 90
b = 136.919	β = 100.26
c = 114.663	γ = 90

Symmetry
Space Group	P 1 21 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	MARMOSAIC 225 mm CCD		2011-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

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	3.02	87.07	88.96	0.112	6.9449	3.8		58488		-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	3.02	3.19	43.15		0.35	2.17	2.06	4120

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 2g03	3.03	15	57892	2943	89.92	0.222	0.222	0.2279	0.248	0.2484	RANDOM	65.684

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]
2.75		1.96	-1.2		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.428
r_dihedral_angle_4_deg	15.971
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_1_deg	4.783
r_scangle_it	2.965
r_scbond_it	1.638
r_angle_refined_deg	1.114
r_mcangle_it	0.95
r_angle_other_deg	0.789
r_mcbond_it	0.425

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.428
r_dihedral_angle_4_deg	15.971
r_dihedral_angle_3_deg	13.491
r_dihedral_angle_1_deg	4.783
r_scangle_it	2.965
r_scbond_it	1.638
r_angle_refined_deg	1.114
r_mcangle_it	0.95
r_angle_other_deg	0.789
r_mcbond_it	0.425
r_mcbond_other	0.061
r_chiral_restr	0.056
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20624
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	496

Software

Software
Software Name	Purpose
SCALA	data scaling
MOSFLM	data reduction
PHASER	phasing
REFMAC	refinement

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.