7XU8 | pdb_00007xu8

Structure of the complex of camel peptidoglycan recognition protein-short (PGRP-S) with heptanoic acid at 2.15 A resolution.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3C2X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	20% glycerol, 6% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.896	α = 90
b = 101.637	β = 90
c = 163.394	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	80	CCD	MAR CCD 165 mm		2011-10-05	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)	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	2.15	43.15	99.71	0.0432	0.95	13.1	6.5		40935			34.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.2	99.7		0.16	0.919	3.8

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	3C2X	2.15	43.15	40935	2035	99.708	0.223	0.2201	0.23	0.2819	0.28	40.642

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]
0.037			-0.25		0.213

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.642
r_dihedral_angle_4_deg	14.106
r_dihedral_angle_3_deg	13.742
r_lrange_it	8.04
r_lrange_other	8.03
r_dihedral_angle_1_deg	7.245
r_scangle_it	5.13
r_scangle_other	5.129
r_mcangle_it	4.552
r_mcangle_other	4.552
r_scbond_it	3.365
r_scbond_other	3.365
r_mcbond_it	3.077
r_mcbond_other	3.075
r_angle_refined_deg	1.425
r_angle_other_deg	1.281
r_metal_ion_refined	0.387
r_nbd_other	0.26
r_xyhbond_nbd_refined	0.217
r_symmetry_xyhbond_nbd_refined	0.212
r_nbd_refined	0.204
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.196
r_nbtor_refined	0.158
r_ncsr_local_group_1	0.089
r_symmetry_xyhbond_nbd_other	0.088
r_ncsr_local_group_3	0.083
r_ncsr_local_group_2	0.08
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_5	0.075
r_ncsr_local_group_6	0.073
r_ncsr_local_group_4	0.072
r_chiral_restr	0.068
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5204
Nucleic Acid Atoms
Solvent Atoms	609
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing