2R1D | pdb_00002r1d

Crystal structure of rat neurexin 1beta in the Ca2+ containing form

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C4R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294	21% Peg 5000 MME, 0.1 M sodium cacodylate pH 6.5, 0.2 M AmSO4, 1.86% 1,2,3-heptanetriol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.683	α = 90
b = 195.719	β = 90
c = 103.867	γ = 90

Symmetry
Space Group	P 21 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	103	CCD	MARRESEARCH		2001-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97949	APS	19-BM

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	2.6	40.6	99.9	0.065	24.8	4.9	73949	73949			51

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.64	99.8		0.423	0.423	4.3	4.7	3636

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	FOURIER SYNTHESIS	THROUGHOUT	1C4R	2.6	20	73564	69823	3741	100	0.20482	0.20482	0.20273	0.21	0.24401	0.25	RANDOM	40.116

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]
2.91			-2.49		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.68
r_dihedral_angle_4_deg	18.155
r_dihedral_angle_3_deg	17.132
r_dihedral_angle_1_deg	7.43
r_scangle_it	2.778
r_scbond_it	1.729
r_angle_refined_deg	1.614
r_mcangle_it	1.143
r_mcbond_it	0.666
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.68
r_dihedral_angle_4_deg	18.155
r_dihedral_angle_3_deg	17.132
r_dihedral_angle_1_deg	7.43
r_scangle_it	2.778
r_scbond_it	1.729
r_angle_refined_deg	1.614
r_mcangle_it	1.143
r_mcbond_it	0.666
r_nbtor_refined	0.313
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.203
r_xyhbond_nbd_refined	0.134
r_metal_ion_refined	0.113
r_symmetry_hbond_refined	0.106
r_chiral_restr	0.101
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12101
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.