2H99

Crystal structure of the effector binding domain of a BenM variant (R156H,T157S)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil		288.2	Precipitant: 0.015 M magnesium acetate, 0.05 M sodium cacodlylate, 1.7 M ammonium sulfate Protein: 20 mM tris HCl, 0.5 M NaCl, pH 7.9, 10% glycerol Equal volumes mixed, microbatch under oil. The growing crystallization solution was in pH 6 and the protein solution was in pH 7.9 condition, temperature 288.2K

Crystal Properties
Matthews coefficient	Solvent content
2.4	49.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.937	α = 90
b = 66.506	β = 90
c = 117.495	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		2005-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	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	1.85	50	99.7	0.073	9.1	5.1		44035

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	1.85	1.92	99.3	99.3	0.484		4.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB accession code 2F97, BenM-EBD (high pH)	1.85	44	43982	41766	2216	99.62	0.167	0.167	0.165	0.204	RANDOM	19.128

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]
1.75			-0.49		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.318
r_dihedral_angle_3_deg	11.159
r_dihedral_angle_4_deg	9.713
r_dihedral_angle_1_deg	5.735
r_scangle_it	3.512
r_scbond_it	2.654
r_mcangle_it	1.306
r_angle_refined_deg	1.085
r_mcbond_it	0.917
r_angle_other_deg	0.731
r_nbd_refined	0.194
r_symmetry_vdw_other	0.173
r_nbd_other	0.169
r_nbtor_refined	0.169
r_symmetry_hbond_refined	0.146
r_symmetry_vdw_refined	0.115
r_xyhbond_nbd_refined	0.113
r_mcbond_other	0.087
r_nbtor_other	0.079
r_chiral_restr	0.059
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	3439
Nucleic Acid Atoms
Solvent Atoms	578
Heterogen Atoms	52

Software

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