3QCW | pdb_00003qcw

Structure of neurexin 1 alpha (domains LNS1-LNS6), no splice inserts

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	5-10% PEG8000 or PEG10000, 2.5 mM calcium chloride, 100 mM bicine, pH 8.0-9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.953	α = 90.61
b = 114.543	β = 90.87
c = 159.581	γ = 92.18

Symmetry
Space Group	P 1

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	MARMOSAIC 300 mm CCD		2010-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D		APS	21-ID-D

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	2.65	50	98.5	0.079	14.5	3.4		124701

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)
1	2.65	2.7	98.2		0.526		3.2	6206

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD, MOLECULAR REPLACEMENT	THROUGHOUT	2.65	30	116726	6451	98.43	0.2093	0.2082	0.2082	0.2296	0.2286	RANDOM	65.5416

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]
-3.76	-1.23	0.31	0.45	0.16	3.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.065
r_dihedral_angle_4_deg	20.474
r_dihedral_angle_3_deg	18.218
r_dihedral_angle_1_deg	7.894
r_scangle_it	3.317
r_scbond_it	2.181
r_angle_refined_deg	1.73
r_mcangle_it	1.222
r_mcbond_it	0.743
r_nbtor_refined	0.321
r_symmetry_hbond_refined	0.252
r_nbd_refined	0.232
r_symmetry_vdw_refined	0.192
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.107
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	15384
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	56

Software

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