5H7D

Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4UOY	4UOY, 2M5A, 3DVE
experimental model	PDB	2M5A	4UOY, 2M5A, 3DVE
experimental model	PDB	3DVE	4UOY, 2M5A, 3DVE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	296	0.1M HEPES pH 7.5, 20.7% PEG 300, 99mM calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.489	α = 84.84
b = 155.376	β = 89.68
c = 155.491	γ = 89.56

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	CCD	ADSC QUANTUM 315		2016-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97934	PAL/PLS	5C (4A)

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	2.6	50	90.5	14.6	2.3		210653

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.69	83.4		1.2	2

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	4UOY, 2M5A, 3DVE	2.57	50	189578	21075	89.49	0.20754	0.20377	0.24092	RANDOM	87.987

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]
4.04	0.33	-0.72	-1.82	2.49	-1.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.544
r_dihedral_angle_4_deg	20.137
r_dihedral_angle_3_deg	16.835
r_sphericity_bonded	14.407
r_long_range_B_refined	6.219
r_rigid_bond_restr	5.384
r_dihedral_angle_1_deg	5.146
r_mcangle_it	4.896
r_scbond_it	4.405
r_mcbond_it	3.686
r_angle_refined_deg	1.232
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_sphericity_free

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	37116
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing