7ESC | pdb_00007esc

FmnB complexed with AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7ESA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		286	0.2 M Potassium sodium tartrate tetrahydrate, 20% w/v Polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.875	α = 90
b = 67.872	β = 90
c = 97.003	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 PILATUS 6M		2020-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.978	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.2	39.46	99	0.0447	0.995	16.63	2		16541

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	2.2	2.279			0.693

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	THROUGHOUT	7ESA	2.201	39.46	16535	847	99.453	0.247	0.2447	0.25	0.282	0.28	51.749

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]
-3.228			2.122		1.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.946
r_dihedral_angle_4_deg	18.134
r_dihedral_angle_3_deg	17.54
r_lrange_it	7.331
r_lrange_other	7.318
r_dihedral_angle_1_deg	6.046
r_scangle_it	4.465
r_scangle_other	4.464
r_mcangle_it	3.396
r_mcangle_other	3.395
r_scbond_it	2.865
r_scbond_other	2.865
r_mcbond_it	2.213
r_mcbond_other	2.213
r_angle_refined_deg	1.415
r_angle_other_deg	1.405
r_symmetry_xyhbond_nbd_refined	0.251
r_xyhbond_nbd_refined	0.207
r_symmetry_nbd_other	0.194
r_nbd_refined	0.186
r_nbtor_refined	0.173
r_nbd_other	0.164
r_symmetry_nbd_refined	0.132
r_symmetry_xyhbond_nbd_other	0.08
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.062
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2510
Nucleic Acid Atoms
Solvent Atoms	125
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
xia2	data reduction
xia2	data reduction
xia2	data scaling
PHASER	phasing