9GFP | pdb_00009gfp

The crystal structure of CsvR from Escherichia coli

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, SITTING DROP		293	20 %w/v PEG3350 0.15 M DL-malic 7 pH 6 %w/v Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.613	α = 90
b = 77.601	β = 90
c = 184.947	γ = 90

Symmetry
Space Group	P 21 21 21

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 16M		2023-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976254	MAX IV	BioMAX

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	3.03	48.32	69.8	0.175	0.183	0.051	0.998	10.1	12.9		8763

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	3.03	3.285	16.6		2.748	2.861	0.791	0.454	1.2	13

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 (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	3.03	48.32	8360	403	69.7	0.21641	0.21225	0.2149	0.29781	0.2877	RANDOM	147.964

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]
-7.42			1.84		5.58

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	19.698
r_long_range_B_other	19.697
r_dihedral_angle_3_deg	18.821
r_scangle_other	11.77
r_mcangle_it	10.513
r_mcangle_other	10.511
r_dihedral_angle_1_deg	8.141
r_dihedral_angle_2_deg	7.66
r_scbond_it	6.984
r_scbond_other	6.983
r_mcbond_it	6.343
r_mcbond_other	6.341
r_angle_refined_deg	1.608
r_angle_other_deg	0.516
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	4047
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms

Software

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