2F6G | pdb_00002f6g

BenM effector binding domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F6P	PDB Entry 2F6P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil		288	PEG 4000, ammonium sulfate, sodium acetate, NaCl, tris, glycerol, imidazole, microbatch under oil, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.412	α = 90
b = 66.615	β = 90
c = 116.549	γ = 90

Symmetry
Space Group	P 21 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	CCD	MARRESEARCH				SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97937	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.908	58.321					29271			27.81656

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	1.9	1.97		22.5	0.434

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 (All)	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 2F6P	1.908	58.321	27770	27770	1461	73.559	0.192	0.19004	0.19	0.2	0.234	0.25	Random	28.476

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]
-0.395			2.568		-2.173

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.409
r_dihedral_angle_4_deg	14.923
r_dihedral_angle_3_deg	13.968
r_dihedral_angle_1_deg	5.937
r_scangle_it	2.79
r_scbond_it	2.1
r_angle_refined_deg	1.226
r_mcangle_it	1.203
r_scangle_other	1.191
r_mcbond_it	0.893
r_scbond_other	0.795
r_angle_other_deg	0.713
r_mcangle_other	0.542
r_nbd_refined	0.176
r_nbtor_refined	0.169
r_nbd_other	0.159
r_symmetry_vdw_other	0.144
r_xyhbond_nbd_refined	0.12
r_symmetry_hbond_refined	0.111
r_symmetry_vdw_refined	0.087
r_nbtor_other	0.079
r_mcbond_other	0.067
r_chiral_restr	0.057
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3503
Nucleic Acid Atoms
Solvent Atoms	579
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing