7XFX

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.28 A resolution.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	10% PEG 3350 0.2M Sodium potassium tartrate 20% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.661	α = 90
b = 101.653	β = 90
c = 163.328	γ = 90

Symmetry
Space Group	I 2 2 2

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 PILATUS3 2M		2018-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.28	78.04	80.68	0.116	0.05	0.998	10.8	6.8		27481

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	2.28	2.32	100		0.828	0.35	0.907	2.5	6.7

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5DWF	2.28	77.921	27481	1341	80.679	0.191	0.1877	0.255	26.517

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]
-0.094			0.046		0.048

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.672
r_dihedral_angle_4_deg	15.994
r_dihedral_angle_3_deg	15.572
r_dihedral_angle_1_deg	7.548
r_lrange_it	5.732
r_lrange_other	5.732
r_scangle_it	3.473
r_scangle_other	3.472
r_mcangle_it	3
r_mcangle_other	2.999
r_scbond_it	2.104
r_scbond_other	2.104
r_mcbond_other	1.775
r_mcbond_it	1.774
r_angle_refined_deg	1.432
r_angle_other_deg	1.269
r_nbd_refined	0.194
r_symmetry_nbd_other	0.194
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.173
r_nbtor_refined	0.159
r_symmetry_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.147
r_symmetry_xyhbond_nbd_other	0.092
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5203
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	77

Software

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