3KUZ | pdb_00003kuz

Crystal structure of the ubiquitin like domain of PLXNC1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H6N	superimposed ensemble of PDB entries 3h6n and 3ig3
experimental model	PDB	3IG3	superimposed ensemble of PDB entries 3h6n and 3ig3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	2.0M ammonium sulfate, 0.2M sodium chloride, 0.1M HEPES, 1:100 w/w chymotrypsin, pH 7.5, vapor diffusion, sitting drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.246	α = 90
b = 72.246	β = 90
c = 116.235	γ = 90

Symmetry
Space Group	P 43 21 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	ADSC QUANTUM 315		2009-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97927	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	20	99.6	0.187	4.1	9		14277

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.34	98.3		0.963		6.2	697

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	superimposed ensemble of PDB entries 3h6n and 3ig3	2.3	20	14229	501	99.762	0.251	0.25	0.2558	0.28	0.2745	thin shells (sftools)	19.04

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]
1.393			1.393		-2.787

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.394
r_dihedral_angle_3_deg	13.937
r_dihedral_angle_1_deg	5.833
r_dihedral_angle_4_deg	3.823
r_scangle_it	3.732
r_scbond_it	2.172
r_mcangle_it	1.695
r_angle_refined_deg	1.466
r_mcbond_it	0.889
r_angle_other_deg	0.843
r_mcbond_other	0.139
r_chiral_restr	0.085
r_bond_refined_d	0.015
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	1608
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	12

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling