7P6F | pdb_00007p6f

1.93 A resolution X-ray crystal structure of the transcriptional regulator SrnR from Streptomyces griseus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3F6V

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE	8.5	293	1 uL of SrnR 12.5 mg mL-1 (in 20 mM TrisHCl PH 7.5, 150 mM NaCl, 1 mM TCEP) were added to 20 uL of volatile oil, immediately followed by 1 uL of precipitant containing 0.2 M calcium acetate hydrate, 0.1 M TrisHCl 8.5, 15 % w/v PEG 4000 (G6 condition of CSSII screening by Molecular Dimensions).

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.358	α = 90
b = 113.358	β = 90
c = 124.943	γ = 120

Symmetry
Space Group	P 62 2 2

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-F		2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97622	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.93	124.94	100	0.126	0.138	0.041	0.999	11.6	11.4		36223			26.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.98	100		1.67	1.827	0.541	0.633	1.5	11.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3F6V	1.93	51.67	36181	1789	99.975	0.18	0.178	0.19	0.2167	0.23	38.772

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]
0.454	0.227		0.454		-1.471

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.194
r_dihedral_angle_4_deg	20.272
r_dihedral_angle_3_deg	15.555
r_lrange_it	7.495
r_lrange_other	7.461
r_dihedral_angle_1_deg	6.172
r_scangle_it	4.527
r_scangle_other	4.526
r_mcangle_it	3.937
r_mcangle_other	3.936
r_scbond_it	2.834
r_scbond_other	2.833
r_mcbond_it	2.489
r_mcbond_other	2.488
r_angle_refined_deg	1.756
r_angle_other_deg	1.45
r_metal_ion_refined	0.257
r_nbd_refined	0.215
r_nbd_other	0.197
r_symmetry_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.16
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.151
r_symmetry_nbd_refined	0.145
r_symmetry_nbtor_other	0.093
r_chiral_restr	0.09
r_symmetry_xyhbond_nbd_other	0.014
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3075
Nucleic Acid Atoms
Solvent Atoms	347
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing