5W70

X-ray Structure of RbmB from Streptomyces ribosidificus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	24-26% PEG-3350, 100 mM MgCl2, 100 mM MOPS, 1 mM PLP, 5 mM 2-DOS

Crystal Properties
Matthews coefficient	Solvent content
2.16	42.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.072	α = 90
b = 101.072	β = 90
c = 160.004	γ = 90

Symmetry
Space Group	P 41 21 2

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	Bruker Platinum 135	montel	2017-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.1	50	99.2	0.092	0.092	10.3	8.3		48736

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	2.1	2.2	98.2		0.375	0.375	2.8	4.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2c7t	2.1	50	46279	2457	99.3	0.18497	0.18236	0.23322	RANDOM	20.551

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]
-1.36			-1.36		2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.209
r_dihedral_angle_4_deg	20.587
r_dihedral_angle_3_deg	17.188
r_dihedral_angle_1_deg	6.778
r_long_range_B_refined	4.791
r_long_range_B_other	4.739
r_scangle_other	3.731
r_scbond_it	2.443
r_scbond_other	2.443
r_mcangle_it	2.408
r_mcangle_other	2.408
r_angle_refined_deg	2.083
r_mcbond_it	1.618
r_mcbond_other	1.617
r_angle_other_deg	1.223
r_chiral_restr	0.118
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6174
Nucleic Acid Atoms
Solvent Atoms	342
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
PHASER	phasing