5XGY | pdb_00005xgy

Crystal structure of peptidoglycan recognition protein (PGRP-S) at 2.45 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	7.2	290	0.3M NaKTartrate, 25% PEG, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.788	α = 90
b = 101.796	β = 90
c = 164.144	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	CCD	MARRESEARCH	Mirror	2016-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.45	86.51	94	0.2	6.74	4.1		26675

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54		71.7	0.825	1.315	3.4

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	2.45	86.51	26675	1362	99.88	0.23661	0.23372	0.24	0.29361	0.3	RANDOM	55.18

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]
8.48			-5.19		-3.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.661
r_long_range_B_refined	13.897
r_dihedral_angle_3_deg	13.833
r_long_range_B_other	13.833
r_dihedral_angle_4_deg	11.642
r_scangle_other	7.87
r_mcangle_it	7.408
r_mcangle_other	7.407
r_dihedral_angle_1_deg	6.269
r_scbond_it	4.863
r_scbond_other	4.858
r_mcbond_it	4.519
r_mcbond_other	4.518
r_angle_refined_deg	1.538
r_angle_other_deg	1.034
r_chiral_restr	0.095
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002
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	5347
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	16

Software

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