27AA | pdb_000027aa

Crystal structure of the complex of short peptidoglycan recognition protein from Camelus dromedarius with nonanoic acid at 1.83 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3O4K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	PEG 3350 Sodium potassium tartarate

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.775	α = 90
b = 101.525	β = 90
c = 163.087	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		2014-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.99	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	1.83	50	99.8	0.06	2	4.3		64628		2

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	1.83	1.86			0.43	2	4.3

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	THROUGHOUT	1.834	34.256	64627	1288	99.751	0.273	0.272	0.2774	0.3211	0.3286	32.334

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]
2.218			-2.616		0.397

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.298
r_dihedral_angle_3_deg	12.237
r_dihedral_angle_2_deg	8.059
r_lrange_it	7.814
r_lrange_other	7.808
r_dihedral_angle_1_deg	6.82
r_scangle_it	5.165
r_scangle_other	5.165
r_mcangle_it	4.275
r_mcangle_other	4.275
r_scbond_it	3.334
r_scbond_other	3.334
r_mcbond_it	2.847
r_mcbond_other	2.847
r_angle_refined_deg	1.436
r_angle_other_deg	0.515
r_symmetry_nbd_refined	0.261
r_nbd_other	0.238
r_xyhbond_nbd_refined	0.22
r_nbd_refined	0.214
r_symmetry_nbd_other	0.208
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.18
r_ncsr_local_group_3	0.104
r_ncsr_local_group_5	0.103
r_ncsr_local_group_1	0.102
r_ncsr_local_group_2	0.096
r_ncsr_local_group_4	0.09
r_ncsr_local_group_6	0.086
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.066
r_bond_refined_d	0.007
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	293
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
autoPROC	data processing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing