9KS0 | pdb_00009ks0

E. coli MaeB PTA domain apo form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZN9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M Ammonium sulfate, 0.05 M ADA, 13% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.066	α = 90
b = 130.026	β = 90
c = 169.981	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		2022-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9000	SPring-8	BL44XU

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	2.8	47.88	99.9	0.181	0.196	0.076	0.995	9.8	6.6		59681			138.04

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	2.8	2.88	100		1.297	1.403	0.531	0.788	1.8	6.9

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	6ZN9	2.8	47.876	59613	2971	99.915	0.216	0.2142	0.2142	0.2592	0.2541	60.271

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]
0.007			-0.018		0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.059
r_dihedral_angle_3_deg	13.771
r_dihedral_angle_4_deg	11.25
r_lrange_it	6.235
r_lrange_other	6.235
r_dihedral_angle_1_deg	4.977
r_mcangle_it	3.434
r_mcangle_other	3.433
r_scangle_it	3.23
r_scangle_other	3.229
r_angle_other_deg	2.275
r_mcbond_it	2.042
r_mcbond_other	2.042
r_scbond_it	1.85
r_scbond_other	1.849
r_angle_refined_deg	1.218
r_nbd_other	0.4
r_symmetry_nbd_refined	0.309
r_symmetry_nbd_other	0.228
r_nbd_refined	0.199
r_nbtor_refined	0.156
r_xyhbond_nbd_refined	0.151
r_symmetry_xyhbond_nbd_other	0.07
r_symmetry_nbtor_other	0.065
r_chiral_restr	0.045
r_bond_other_d	0.034
r_gen_planes_other	0.009
r_bond_refined_d	0.005
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15407
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	10

Software

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