3C2X | pdb_00003c2x

Crystal structure of peptidoglycan recognition protein at 1.8A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YCK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	50mm Tris-HCl, 20% PEG3350, 0.2M Na-K Tartarate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.044	α = 90
b = 101.898	β = 90
c = 162.675	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	203	IMAGE PLATE	MAR scanner 345 mm plate		2007-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.93	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.8	19.93	99.8			64315	63669			24.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	19.9	99.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1yck	1.83	19.93	64315	63669	1595	99.4	0.23	0.225	0.225	0.24	0.247	0.25	RANDOM	36.2

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]
15.25			-11.24		-4.02

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	24.5
c_angle_deg	2
c_scangle_it	1.66
c_mcangle_it	1.61
c_improper_angle_d	1.5
c_scbond_it	1.09
c_mcbond_it	0.95
c_bond_d	0.014
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5348
Nucleic Acid Atoms
Solvent Atoms	739
Heterogen Atoms	93

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data collection
MOSFLM	data reduction
SCALEPACK	data scaling
AMoRE	phasing