2F6P | pdb_00002f6p

BenM effector binding domain- SeMet derivative

X-RAY DIFFRACTION

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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 = 65.09	α = 90
b = 66.702	β = 90
c = 117.849	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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.97935	APS	22-ID

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	58.926	99.6	0.069	49.6	11.4		35252			24.31766

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	2.07	98.6	98.6	0.221	9.6		3427

Refinement

Statistics
Diffraction ID	Structure Solution Method	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	SAD	2.001	58.926	33427	35170	1743	99.451	0.183	0.183	0.1811	0.19	0.2267	0.2391	Random	26.413

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]
3.688			-0.832		-2.856

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.062
r_dihedral_angle_4_deg	14.747
r_dihedral_angle_3_deg	13.523
r_dihedral_angle_1_deg	5.792
r_scangle_it	3.831
r_scbond_it	2.541
r_scangle_other	1.731
r_mcangle_it	1.55
r_angle_refined_deg	1.048
r_mcbond_it	0.732
r_angle_other_deg	0.719
r_scbond_other	0.701
r_mcangle_other	0.697
r_symmetry_vdw_other	0.208
r_nbd_refined	0.178
r_nbtor_refined	0.166
r_symmetry_hbond_refined	0.166
r_nbd_other	0.163
r_symmetry_vdw_refined	0.119
r_xyhbond_nbd_refined	0.116
r_nbtor_other	0.079
r_mcbond_other	0.069
r_chiral_restr	0.061
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	3532
Nucleic Acid Atoms
Solvent Atoms	487
Heterogen Atoms	15

Software

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