6A89 | pdb_00006a89

Crystal structure of the ternary complex of peptidoglycan recognition protein (PGRP-S) with Tartaric acid, Ribose and 2,6-DIAMINOPIMELIC ACID at 2.11 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q8S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	10% PEG 3350, 0.2M Sodium potassium tartarate

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.5	α = 90
b = 101.37	β = 90
c = 163.04	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	298	PIXEL	DECTRIS PILATUS3 6M		2018-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.9537	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.11	86.09	100	0.09	0.1	3.05	6.6		42613			38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.17	100		0.74	0.81		6.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4Q8S	2.11	86.09	40430	2161	99.95	0.19365	0.19067	0.2	0.24884	0.25	RANDOM	47.707

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]
5.65			-4.09		-1.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.263
r_dihedral_angle_4_deg	15.17
r_dihedral_angle_3_deg	13.937
r_long_range_B_refined	8.554
r_long_range_B_other	8.553
r_dihedral_angle_1_deg	7.304
r_scangle_other	6.601
r_mcangle_it	5.066
r_mcangle_other	5.066
r_scbond_it	4.481
r_scbond_other	4.481
r_mcbond_it	3.59
r_mcbond_other	3.59
r_angle_refined_deg	1.766
r_angle_other_deg	1.073
r_chiral_restr	0.106
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5223
Nucleic Acid Atoms
Solvent Atoms	293
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing