2YJT | pdb_00002yjt

Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q5X	PDB ENTRY 1Q5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	289	CRYSTALS WERE PREPARED USING THE HANGING DROP METHOD AT 16 DEG. C BY MIXING 1:1 PROTEIN SAMPLE WITH MOTHER LIQUOR: 100 MM MAGNESIUM ACETATE, 100 MM MOPS PH 7.2 AND 12% W/V PEG 8000.THE CRYSTALS WERE TRANSFERRED BRIEFLY TO RESERVOIR SOLUTION SUPPLEMENTED WITH 25% (V/V) GLYCEROL AND FLASH FROZEN IN LIQUID NITROGEN.

Crystal Properties
Matthews coefficient	Solvent content
2.47	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.39	α = 90
b = 73.39	β = 90
c = 222.891	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 CCD	MIRRORS	2010-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04		Diamond	I04

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	2.9	63.56	99.6	0.12	10.2	4		15208		6

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	2.9	3.06	99.5		0.51	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 (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 1Q5X	2.9	74.3	15208	804	99.07	0.19544	0.19227	0.2	0.25658	0.25	RANDOM	39.431

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]
0.97	0.48		0.97		-1.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.334
r_dihedral_angle_4_deg	21.774
r_dihedral_angle_3_deg	20.397
r_dihedral_angle_1_deg	7.124
r_scangle_it	3.107
r_scbond_it	1.742
r_angle_refined_deg	1.59
r_mcangle_it	1.31
r_mcbond_it	0.674
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4964
Nucleic Acid Atoms
Solvent Atoms	29
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing