8BJP | pdb_00008bjp

The N288D mutant cytoplasmic PAS domain of Geobacillus thermodenitrificans histidine kinase CitA

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.4M magnesium chloride, 0.1M Tris/HCl, pH 8.5, 20.5% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.166	α = 90
b = 49.295	β = 90
c = 92.199	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 6M		2013-12-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97957, 0.9800, 0.97188	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	43.509	92.1	0.038	20.96	3.12		12630

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	2.1	2.15			0.267

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	MAD	FREE R-VALUE	2.1	43.509	12630	640	92.203	0.197	0.1951	0.2	0.2326	0.24	42.09

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]
-0.255			-0.347		0.602

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.302
r_dihedral_angle_4_deg	16.077
r_dihedral_angle_3_deg	14.512
r_lrange_it	9.475
r_lrange_other	9.456
r_scangle_it	7.897
r_scangle_other	7.893
r_dihedral_angle_1_deg	6.95
r_scbond_it	5.329
r_scbond_other	5.325
r_mcangle_other	4.91
r_mcangle_it	4.909
r_mcbond_it	3.716
r_mcbond_other	3.676
r_angle_refined_deg	1.614
r_angle_other_deg	1.324
r_symmetry_xyhbond_nbd_refined	0.257
r_nbd_refined	0.206
r_nbd_other	0.206
r_symmetry_nbd_other	0.185
r_nbtor_refined	0.15
r_xyhbond_nbd_refined	0.136
r_symmetry_nbd_refined	0.099
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.068
r_metal_ion_refined	0.042
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1594
Nucleic Acid Atoms
Solvent Atoms	33
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SADABS	data scaling
SHELXDE	phasing