5ZNJ | pdb_00005znj

Crystal structure of a bacterial ProRS with ligands

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J3L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	297	32 - 40% (v/v) Pentaerythritol propoxylate (5/4 PO/OH), 0.1 - 0.2 M KCl and 50 mM HEPES, pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.139	α = 90
b = 77.535	β = 99.36
c = 74.226	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 315r		2017-03-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.98	SSRF	BL17U1

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	1.84	50	98.5	0.051	34.6	3.1		62796

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	1.84	1.91	99.9		0.488	2.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2J3L	1.84	50	59229	3053	98.45	0.19852	0.19728	0.2	0.22249	0.23	RANDOM	43.912

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]
-1.05		0.72	1.62		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.598
r_dihedral_angle_4_deg	13.429
r_dihedral_angle_3_deg	12.077
r_dihedral_angle_1_deg	5.886
r_long_range_B_refined	4.407
r_long_range_B_other	4.407
r_mcangle_it	1.39
r_mcangle_other	1.39
r_scangle_other	1.297
r_angle_refined_deg	1.175
r_angle_other_deg	0.854
r_mcbond_it	0.795
r_mcbond_other	0.795
r_scbond_it	0.74
r_scbond_other	0.74
r_chiral_restr	0.064
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.002
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	4384
Nucleic Acid Atoms
Solvent Atoms	273
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing