2VV5 | pdb_00002vv5

The open structure of MscS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2OAU	PDB ENTRY 2OAU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		THE BEST CRYSTALS (BY VISUAL INSPECTION) WERE OBTAINED USING 0.1M HEPES PH 7.2, 0.2 M SODIUM FORMATE, 14 % PEG3350, 8 % GLYCEROL AS PRECIPITANT. PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO A SOLUTION CONTAINING 40MM TRIS PH 7.5, 0.01% FOS-CHOLINE-14, 0.15 M NACL, 0.3 M SODIUM FORMATE, 20% GLYCEROL AND 22% PEG3350.

Crystal Properties
Matthews coefficient	Solvent content
4.7	73.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 230.88	α = 90
b = 126.62	β = 90.42
c = 123.22	γ = 90

Symmetry
Space Group	C 1 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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	3.45	37	99	0.08	12	4.2		46433

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	3.45	3.55	99		0.8	1.8	4

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 2OAU	3.45	123.09	44094	2336	99	0.294	0.293	0.26	0.312	0.28	RANDOM	92.6

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]
-0.67		10.14	-3.68		4.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.27
r_dihedral_angle_4_deg	18.399
r_dihedral_angle_3_deg	18.076
r_dihedral_angle_1_deg	6.367
r_angle_refined_deg	1.247
r_scangle_it	1.078
r_angle_other_deg	0.925
r_scbond_it	0.721
r_mcangle_it	0.476
r_symmetry_vdw_other	0.469
r_mcbond_it	0.435
r_symmetry_hbond_refined	0.433
r_symmetry_vdw_refined	0.368
r_nbd_refined	0.238
r_nbtor_refined	0.186
r_nbd_other	0.184
r_xyhbond_nbd_refined	0.133
r_nbtor_other	0.082
r_chiral_restr	0.07
r_bond_refined_d	0.012
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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	13692
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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