8BRF | pdb_00008brf

YopQ apo from Yersinia enterocolitica

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris-HCl, 2M AmSO4

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.492	α = 90
b = 75.176	β = 90
c = 166.65	γ = 90

Symmetry
Space Group	I 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		2021-09-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976200	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	2.74	48.51	100	0.188	0.195	0.053	0.998	11.8	13.1		10860

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	2.74	2.87	100		2.666	2.769	0.745	0.49		13.3

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	AF-P27474-F1	2.74	48.505	10860	533	99.926	0.233	0.2314	0.24	0.267	0.28	66.686

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]
4.934			-1.697		-3.237

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	43.306
r_dihedral_angle_4_deg	22.718
r_dihedral_angle_3_deg	21.041
r_lrange_it	13.032
r_lrange_other	13.031
r_scangle_it	9.178
r_scangle_other	9.036
r_mcangle_it	7.22
r_mcangle_other	7.22
r_dihedral_angle_1_deg	7.038
r_scbond_it	5.923
r_scbond_other	5.888
r_mcbond_it	4.767
r_mcbond_other	4.731
r_angle_refined_deg	1.534
r_angle_other_deg	1.509
r_nbd_other	0.382
r_symmetry_nbd_refined	0.374
r_symmetry_xyhbond_nbd_refined	0.306
r_symmetry_nbd_other	0.213
r_nbd_refined	0.205
r_ncsr_local_group_1	0.194
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.174
r_symmetry_xyhbond_nbd_other	0.16
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2262
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms	17

Software

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