9UGE | pdb_00009uge

Crystal structure of the complex of camel peptidoglycan recognition protein, PGRP-S with malic acid and oxalic acid at 2.3 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q9E

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
2.41	48.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.308	α = 90
b = 101.623	β = 90
c = 162.683	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	77	CCD	MARRESEARCH		2014-02-12	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	2.305	40.704	89.2	0.074	9.8	1		29076			44.6

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	2.305	2.34			0.668

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.305	40.704	29076	700	88.909	0.216	0.2147	0.2198	0.2833	0.2815	55.996

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]
7.997			-6.24		-1.757

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.914
r_dihedral_angle_3_deg	13.842
r_lrange_it	10.513
r_lrange_other	10.512
r_dihedral_angle_1_deg	7.574
r_scangle_it	6.004
r_scangle_other	6.002
r_mcangle_it	5.718
r_mcangle_other	5.718
r_dihedral_angle_2_deg	5.118
r_scbond_it	3.596
r_scbond_other	3.594
r_mcbond_it	3.467
r_mcbond_other	3.466
r_angle_refined_deg	1.235
r_angle_other_deg	0.448
r_symmetry_nbd_other	0.215
r_nbd_refined	0.211
r_nbd_other	0.21
r_symmetry_nbd_refined	0.205
r_xyhbond_nbd_refined	0.2
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.062
r_chiral_restr	0.059
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5348
Nucleic Acid Atoms
Solvent Atoms	371
Heterogen Atoms	21

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
AMoRE	phasing
DENZO	data reduction
SCALEPACK	data scaling
Coot	model building