7XFY | pdb_00007xfy

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.67 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DWF

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
2.43	49.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.583	α = 90
b = 101.026	β = 90
c = 163.412	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	2.67	85.93	91.49	0.113	0.06	0.994	12.6	4.4		19639

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	2.67	2.71	90		0.718	0.367	0.776	4.6	4.6

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	5DWF	2.67	85.93	19639	961	91.502	0.18	0.1754	0.18	0.2657	0.27	33.021

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]
-0.176			0.169		0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.448
r_dihedral_angle_4_deg	19.928
r_dihedral_angle_3_deg	18.936
r_lrange_it	10.033
r_lrange_other	10.033
r_dihedral_angle_1_deg	7.788
r_scangle_it	5.631
r_scangle_other	5.63
r_mcangle_it	4.786
r_mcangle_other	4.786
r_scbond_it	3.592
r_scbond_other	3.591
r_mcbond_it	3.053
r_mcbond_other	3.049
r_angle_refined_deg	1.65
r_angle_other_deg	1.264
r_symmetry_nbd_refined	0.22
r_symmetry_nbd_other	0.206
r_nbd_refined	0.203
r_nbd_other	0.2
r_xyhbond_nbd_refined	0.185
r_symmetry_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.166
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.072
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5203
Nucleic Acid Atoms
Solvent Atoms	349
Heterogen Atoms	73

Software

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