9LTH | pdb_00009lth

Crystal structure of transcriptional regulator (NrpR) from Streptococcus salivarius K12

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		295	0.1 M Bis-Tris propane (pH 7.95), 0.7 M Sodium Citrate tribasic dihydrate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.747	α = 90
b = 128.26	β = 100.616
c = 72.63	γ = 90

Symmetry
Space Group	I 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	PIXEL	DECTRIS EIGER X 9M		2022-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9797	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.59	36.705	97.4	0.99	11.8	2.5		9474

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.59	2.71			0.95

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	MOLECULAR REPLACEMENT	FREE R-VALUE	2.59	36.705	9474	458	97.199	0.187	0.1834	0.1908	0.2659	0.2782	76.112

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]
-0.05		-0.017	0.011		0.042

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.21
r_dihedral_angle_3_deg	17.895
r_dihedral_angle_4_deg	16.789
r_lrange_it	16.507
r_lrange_other	16.502
r_scangle_it	10.258
r_scangle_other	10.255
r_mcangle_other	9.576
r_mcangle_it	9.575
r_scbond_it	6.737
r_mcbond_it	6.735
r_scbond_other	6.734
r_mcbond_other	6.706
r_dihedral_angle_1_deg	6.127
r_angle_refined_deg	1.454
r_angle_other_deg	1.239
r_symmetry_xyhbond_nbd_refined	0.248
r_nbd_other	0.24
r_nbd_refined	0.204
r_symmetry_nbd_other	0.201
r_symmetry_nbd_refined	0.19
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.155
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2378
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms

Software

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