5M1T

PaMucR Phosphodiesterase, c-di-GMP complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R6O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	294	0.055M MES, 0.045M Imidazole, 12.5% PEG 1000, 12.5% PEG3350, 12.5% MPD, 0.03M diethyleneglycol, 0.03M triethyleneglycol, 0.03M tetraethyleneglycol, 0.03M pentaethyleneglycol

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.37	α = 90
b = 116.11	β = 102.52
c = 52.14	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS 6M		2014-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.27	45.27	99.9	0.167	0.994	11.3	6.9		24883

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.27	2.33	99.8		0.677	0.853	2.9	6.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2R6O	2.27	45.27	23617	1249	99.92	0.1975	0.19527	0.23821	RANDOM	35.452

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]
-0.73		0.52	-0.21		0.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.947
r_dihedral_angle_4_deg	17.879
r_dihedral_angle_3_deg	12.888
r_dihedral_angle_1_deg	5.446
r_long_range_B_refined	4.073
r_long_range_B_other	4.041
r_scangle_other	1.797
r_mcangle_it	1.661
r_mcangle_other	1.66
r_angle_refined_deg	1.44
r_scbond_it	1.064
r_scbond_other	1.059
r_mcbond_it	0.976
r_mcbond_other	0.975
r_angle_other_deg	0.71
r_chiral_restr	0.068
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3563
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	96

Software

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