3K1N | pdb_00003k1n

Crystal Structure of full-length BenM

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F97	PDB entry 2F97

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER OIL	9	295	Precipitant: 35% v/v iso-propanol, 0.1 M Tris HCl pH 8.5, 0.2 M Ammonium acetate. Protein: 30 mM Tris base pH 9.0, 0.5 M NaCl, 10% glycerol, 250 mM imidazole, 10 mM BME, MICROBATCH UNDER OIL, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.24	α = 90
b = 70.1	β = 90
c = 187.87	γ = 90

Symmetry
Space Group	P 2 2 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	MAR CCD 165 mm		2008-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	1.00800	APS	19-ID

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	2.99	50	87.2	0.076	0.076	15.4	4.7		17220			32.715

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)
	2.99	3.11	90		0.304	0.304	4.09	4.4	1732

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 2F97	2.99	39.04	16796	16796	875	86.85	0.156	0.156	0.155	0.2187	0.18	0.2437	RANDOM	32.715

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]
7.89			16.23		-24.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.754
r_dihedral_angle_3_deg	17.325
r_dihedral_angle_4_deg	15.351
r_dihedral_angle_1_deg	5.389
r_mcangle_it	3.87
r_mcbond_it	2.517
r_scangle_it	1.525
r_angle_refined_deg	1.221
r_scbond_it	0.943
r_chiral_restr	0.093
r_bond_refined_d	0.009
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4860
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing