6ZR7

X-ray structure of human Dscam Ig7-Ig9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WVR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	292	Glycerol, calcium acetate, PEG 8000, HEPES

Crystal Properties
Matthews coefficient	Solvent content
3.48	64.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.599	α = 90
b = 71.421	β = 113.061
c = 92.174	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	PIXEL	DECTRIS PILATUS 6M		2017-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976300	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.85	84.81	99	0.044	0.051	0.026	1	12.8	3.8		39662			36.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.89	97.4		0.874	1.011	0.501	0.7

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4wvr	1.85	84.808	39659	2001	98.782	0.196	0.1947	0.228	56.811

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]
-1.329		1.17	0.428		-0.069

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.117
r_dihedral_angle_4_deg	15.353
r_dihedral_angle_3_deg	13.846
r_lrange_it	11.9
r_lrange_other	11.898
r_scangle_it	9.867
r_scangle_other	9.865
r_dihedral_angle_1_deg	7.64
r_mcangle_it	7.219
r_mcangle_other	7.217
r_scbond_it	6.844
r_scbond_other	6.841
r_mcbond_other	5.483
r_mcbond_it	5.482
r_angle_refined_deg	1.85
r_angle_other_deg	1.321
r_symmetry_nbd_refined	0.248
r_nbd_other	0.207
r_symmetry_nbd_other	0.197
r_nbd_refined	0.193
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.122
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.08
r_symmetry_metal_ion_refined	0.042
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2270
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing