3BOP | pdb_00003bop

Structure of mouse beta-neurexin 2D4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	15% PEG 4000, 0.2M (NH4)2SO4, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.485	α = 90
b = 96.983	β = 105.98
c = 62.584	γ = 90

Symmetry
Space Group	C 1 2 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	MAR CCD 165 mm	Si111	2006-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4C	0.9793	NSLS	X4C

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	3	30	98.7	0.116	6.5	3.3		10939

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	3	3.11	99.6		0.43	2	3.4	1116

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		THROUGHOUT	3	20	10871	546	98.61	0.215	0.211	0.2181	0.289	0.2244	RANDOM	43.601

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]
-0.23		1.82	-2.58		3.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.514
r_dihedral_angle_3_deg	18.109
r_dihedral_angle_4_deg	17.347
r_dihedral_angle_1_deg	5.582
r_angle_refined_deg	1.029
r_scangle_it	0.617
r_scbond_it	0.359
r_mcangle_it	0.311
r_nbtor_refined	0.308
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.171
r_mcbond_it	0.17
r_symmetry_hbond_refined	0.148
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3871
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing