7SZ8 | pdb_00007sz8

Crystal structure of human CELSR1 EC4-7

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5T9T	5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4
experimental model	PDB	5SZN	5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4
experimental model	PDB	5V5X	5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4
experimental model	PDB	6C13	5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4
experimental model	PDB	6E6B	5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4
experimental model	PDB	6VG4	5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1 M magnesium chloride, 0.1 M MES pH 7.3, 30% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.384	α = 89.834
b = 76.943	β = 87.776
c = 92.742	γ = 76.235

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	PIXEL	DECTRIS EIGER2 X 16M		2020-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97911	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.337	46.378	85.3	0.992	15.375	3.3		47823

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.337	2.39	82.5		0.984	8.824	3.2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5t9t, 5szn, 5v5x, 6c13, 6e6b, 6vg4	2.337	46.378	40785	1974	84.627	0.217	0.2133	0.22	0.2794	0.28	37.087

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]
-2.333	2.056	-3.349	-4.996	3.032	8.536

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.649
r_dihedral_angle_4_deg	19.575
r_dihedral_angle_3_deg	15.195
r_dihedral_angle_1_deg	8.649
r_lrange_it	2.959
r_lrange_other	2.916
r_angle_refined_deg	1.752
r_mcangle_it	1.596
r_mcangle_other	1.596
r_scangle_it	1.53
r_scangle_other	1.53
r_angle_other_deg	1.23
r_mcbond_it	0.958
r_mcbond_other	0.957
r_scbond_it	0.929
r_scbond_other	0.929
r_nbd_refined	0.226
r_nbd_other	0.194
r_symmetry_nbd_other	0.184
r_symmetry_nbd_refined	0.174
r_xyhbond_nbd_refined	0.172
r_metal_ion_refined	0.168
r_nbtor_refined	0.158
r_symmetry_xyhbond_nbd_other	0.095
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_refined	0.068
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6472
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	20

Software

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