9T28 | pdb_00009t28

WspR response regulator with crystallization epitope mutations G306D:G308D

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I5B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2M lithium sulfate 25% PEG3350 0.1M bis-tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
1.77	30.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.12	α = 90
b = 45.4	β = 90
c = 85.23	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 2M		2015-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91739	Diamond	I04-1

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	1.2	42.615	89.6	0.021	20.5	5.7		37725

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.23			0.829

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.33	42.615	30751	1504	98.605	0.166	0.1639	0.1638	0.2133	0.2131	17.801

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]
-0.41			-0.035		0.445

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.453
r_lrange_it	13.309
r_lrange_other	12.931
r_dihedral_angle_3_deg	11.558
r_scangle_it	9.886
r_scangle_other	9.886
r_scbond_it	7.019
r_scbond_other	7.015
r_dihedral_angle_2_deg	6.751
r_mcangle_other	6.549
r_mcangle_it	6.543
r_dihedral_angle_1_deg	6.133
r_mcbond_it	4.661
r_mcbond_other	4.628
r_rigid_bond_restr	3.778
r_angle_refined_deg	1.801
r_angle_other_deg	0.771
r_nbd_refined	0.234
r_nbd_other	0.194
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.166
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_refined	0.128
r_chiral_restr	0.098
r_symmetry_nbtor_other	0.072
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1304
Nucleic Acid Atoms
Solvent Atoms	74
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing