7XFW | pdb_00007xfw

Crystal structure of the ternary complex of Peptidoglycan recognition protein, PGRP-S with hexanoic and tartaric acids at 2.07 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
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.889	α = 90
b = 101.508	β = 90
c = 162.996	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	0.97	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.07	46.36	99.82	0.041	0.99	8.13	6.94		45175

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	2.12	99.79		0.433	0.869	1.9	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	2.07	46.358	45174	1297	99.817	0.202	0.1998	0.21	0.2576	0.26	36.53

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]
0.018			-0.021		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.479
r_dihedral_angle_3_deg	15.165
r_dihedral_angle_4_deg	14.04
r_dihedral_angle_1_deg	7.39
r_lrange_it	6.74
r_lrange_other	6.738
r_scangle_it	4.877
r_scangle_other	4.877
r_mcangle_it	3.878
r_mcangle_other	3.877
r_scbond_it	3.157
r_scbond_other	3.156
r_mcbond_it	2.71
r_mcbond_other	2.709
r_angle_refined_deg	1.498
r_angle_other_deg	1.351
r_symmetry_xyhbond_nbd_refined	0.23
r_symmetry_nbd_other	0.2
r_nbd_refined	0.199
r_xyhbond_nbd_refined	0.189
r_nbd_other	0.188
r_nbtor_refined	0.162
r_symmetry_nbd_refined	0.16
r_symmetry_xyhbond_nbd_other	0.134
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.075
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
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	467
Heterogen Atoms	81

Software

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