3Q64 | pdb_00003q64

X-ray crystal structure of protein mll3774 from Mesorhizobium loti, Northeast Structural Genomics Consortium Target MlR405.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6	277	Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM MES (pH 6), PEG 4000 20% (w/v),100 mM Magnesium sulfate heptahydrate, Microbatch, under oil, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.37	63.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.378	α = 90
b = 86.378	β = 90
c = 57.69	γ = 120

Symmetry
Space Group	P 32 2 1

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	ADSC QUANTUM 4	mirrors	2010-10-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.97897	NSLS	X4A

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	1.5	30	99.1	0.047	0.04	50.2	11.2	77329	76634			17.7

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)
1	1.5	1.55	100		0.423	0.338	5.6	11.1	7716

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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	THROUGHOUT	1.5	20	35963	35963	3993	100	0.179	0.17864	0.17684	0.1933	0.19486	0.2073	RANDOM	21.27

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]
0.8	0.4		0.8		-1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.987
r_dihedral_angle_4_deg	15.913
r_dihedral_angle_3_deg	11.382
r_dihedral_angle_1_deg	5.63
r_sphericity_free	3.43
r_scangle_it	3.21
r_scbond_it	2.273
r_sphericity_bonded	2.046
r_mcangle_it	1.397
r_rigid_bond_restr	1.38
r_angle_refined_deg	1.184
r_mcbond_it	1.014
r_nbtor_refined	0.312
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.181
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1221
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SHELX	model building
CNS	refinement
ADSC	data collection
CNS	refinement
XTALVIEW	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing