5KGO | pdb_00005kgo

Structure of K. pneumonia MrkH-c-di-GMP complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	20% PEG 3350, 0.1 M Bis tris propane/HCl pH 6.5, 0.2 M sodium fluoride.

Crystal Properties
Matthews coefficient	Solvent content
3.02	59.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.573	α = 90
b = 74.569	β = 90
c = 135.538	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	CCD	ADSC QUANTUM 315r		2016-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	37.285	94.1	5.2	3.2		14247

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	96.5		0.8	1.2	3.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MAD	FREE R-VALUE	2.9	37.285	1.35	14120	1413	92.3	0.2318	0.2257	0.2199	0.2887	0.2852	97.68

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]
-12.8661			24.9129		-12.0469

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	40.688
f_angle_d	1.721
f_chiral_restr	0.06
f_plane_restr	0.045
f_bond_d	0.028

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3688
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	184

Software

Software
Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
SOLVE	phasing
RESOLVE	model building
PDB_EXTRACT	data extraction