9G9Q | pdb_00009g9q

Crystal structure of PbdA bound to p-methoxybenzoate.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DNJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M HEPES pH 7.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.17	α = 99.87
b = 55.11	β = 94.9
c = 64.26	γ = 103.24

Symmetry
Space Group	P 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 EIGER2 XE 16M		2022-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.03	52.595	97.92	0.1713	0.99	6.1	3.57		43063

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.07	96.46		1.553	0.95	0.304	0.75	3.6

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	2.03	52.595	43061	2174	97.915	0.169	0.1641	0.1751	0.2575	0.2601	23.606

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]
0.466	-1.038	-0.113	-0.509	-0.878	0.944

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.31
r_dihedral_angle_3_deg	14.933
r_lrange_it	14.786
r_lrange_other	14.482
r_dihedral_angle_2_deg	13.652
r_scangle_it	10.458
r_scangle_other	10.456
r_mcangle_it	10.27
r_mcangle_other	10.269
r_scbond_it	7.196
r_scbond_other	7.195
r_dihedral_angle_1_deg	7.09
r_mcbond_it	6.979
r_mcbond_other	6.979
r_rigid_bond_restr	4.986
r_angle_refined_deg	2.202
r_angle_other_deg	0.901
r_symmetry_xyhbond_nbd_refined	0.221
r_nbd_refined	0.203
r_symmetry_nbd_refined	0.188
r_nbd_other	0.179
r_nbtor_refined	0.171
r_symmetry_nbd_other	0.164
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.113
r_ncsr_local_group_1	0.098
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6014
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	150

Software

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