3K1M | pdb_00003k1m

Crystal Structure of full-length BenM, R156H mutant

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		295	5mcL precipitant and 4 mcL protein solution. Precipitant: 80% Crystal Screen 2 (CS-2, Hampton Research) condition 31, 20% CS-2 condition 26 Protein: 30 mM Tris, 0.5 M NaCl, 10% glycerol, 250 mM imidazole, 10 mM mercaptolethanol, pH 9.0, MICROBATCH UNDER OIL, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.24	62.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.997	α = 90
b = 70.789	β = 90
c = 186.275	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		2009-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97934	APS	19-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	2.29	100	99.6	0.071	13.7	5.6		41907			25.981

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)
	2.29	2.34	100		0.507	0.507	3.81	5.7	2078

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2F97	2.29	49.77	41729	41729	2116	97.84	0.148	0.148	0.147	0.179	0.2389	RANDOM	25.981

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]
9.18			15.41		-24.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.775
r_dihedral_angle_4_deg	14.267
r_dihedral_angle_3_deg	13.942
r_dihedral_angle_1_deg	4.949
r_mcangle_it	2.746
r_mcbond_it	1.987
r_scangle_it	1.369
r_angle_refined_deg	1.037
r_scbond_it	0.956
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4836
Nucleic Acid Atoms
Solvent Atoms	508
Heterogen Atoms	24

Software

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