5CMT | pdb_00005cmt

Fic protein from Neisseria meningitidis (NmFic) mutant E156R Y183F in dimeric form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5CKL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	7.8	277.15	10 mM Tris pH 7.8, 100 mM NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.74	54.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.375	α = 90
b = 50.697	β = 90
c = 129.778	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 2M		2013-02-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.8000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	0.99	47.22	96.8	0.04	0.017	0.999	23.4	6.4		126436

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	0.99	1.01	89.6		0.6	0.254	0.783	3	6.4	5729

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	5CKL	0.99	47.22	120051	6297	96.6	0.1354	0.1343	0.14	0.1553	0.16	RANDOM	11.055

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]
-0.3			0.42		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.959
r_sphericity_free	25.102
r_dihedral_angle_4_deg	13.356
r_dihedral_angle_3_deg	12.848
r_sphericity_bonded	9.717
r_rigid_bond_restr	6.322
r_dihedral_angle_1_deg	5.548
r_angle_refined_deg	2.088
r_mcangle_it	1.659
r_mcbond_it	1.458

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.959
r_sphericity_free	25.102
r_dihedral_angle_4_deg	13.356
r_dihedral_angle_3_deg	12.848
r_sphericity_bonded	9.717
r_rigid_bond_restr	6.322
r_dihedral_angle_1_deg	5.548
r_angle_refined_deg	2.088
r_mcangle_it	1.659
r_mcbond_it	1.458
r_mcbond_other	1.227
r_angle_other_deg	1.053
r_chiral_restr	0.119
r_bond_refined_d	0.025
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1488
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

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.