2Q9L | pdb_00002q9l

Crystal structure of iMazG from Vibrio DAT 722: Ctag-iMazG (P43212)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Q73	PDB ENTRY 2Q73

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.05	293	0.1 M sodium citrate, 1.9 M ammonium sulfate, 500 mM NaCl, 10% 2-methyl-2,4-pentanediol, 10 mM MgCl2, pH 5.05, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.246	α = 90
b = 88.246	β = 90
c = 159.107	γ = 90

Symmetry
Space Group	P 43 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	MARMOSAIC 300 mm CCD	SI(111) DOUBLE CRYSTAL MONOCHROMETER	2007-03-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D		APS	23-ID-D

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	2.2	77.171	94.8	0.117	0.117	4	3.6		30948

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	2.2	2.32	71.6		0.578	0.578	1.2	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 2Q73	2.2	36.27	30886	29321	1565	94.5	0.219	0.218	0.22	0.24	0.24	RANDOM	39.73

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]
0.81			0.81		-1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.159
r_dihedral_angle_3_deg	13.661
r_dihedral_angle_4_deg	6.095
r_dihedral_angle_1_deg	5.427
r_scangle_it	2.312
r_scbond_it	1.444
r_angle_refined_deg	1.21
r_mcangle_it	0.824
r_mcbond_it	0.435
r_nbtor_refined	0.302
r_symmetry_hbond_refined	0.219
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.187
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.087
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2719
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	4

Software

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