8AXC | pdb_00008axc

Crystal structure of mouse Ces2c

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MX9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Crystallisation condition 0.5 ul with PEG 8000, 0.2 M Ammonium sulfate 0.1 M Sodium cacodylate, pH-6.5, 30 % w/v and 0.5 ul 10mg/ml Protein in 150mM NaCl, 20mM Tris HCl

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.052	α = 90
b = 143.595	β = 90
c = 183.756	γ = 90

Symmetry
Space Group	P 21 21 21

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		2021-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.012100	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.12	49.05	98.99	0.0906	0.998	15.23	6.9		145761

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.196	97.4		0.5328	0.881		6.3

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	1MX9	2.12	49.05	145757	7342	99.004	0.165	0.163	0.17	0.1959	0.2	33.15

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]
0.009			0.008		-0.017

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.54
r_dihedral_angle_4_deg	18.778
r_dihedral_angle_3_deg	11.596
r_lrange_it	8.16
r_lrange_other	8.093
r_dihedral_angle_1_deg	6.685
r_scangle_it	6.358
r_scangle_other	6.357
r_mcangle_other	4.247
r_mcangle_it	4.246
r_scbond_it	4.097
r_scbond_other	4.096
r_mcbond_it	2.951
r_mcbond_other	2.948
r_angle_other_deg	2.303
r_angle_refined_deg	1.534
r_nbd_other	0.265
r_symmetry_nbd_refined	0.256
r_nbd_refined	0.221
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.132
r_ncsr_local_group_1	0.09
r_chiral_restr	0.083
r_ncsr_local_group_2	0.078
r_ncsr_local_group_3	0.078
r_ncsr_local_group_4	0.078
r_ncsr_local_group_6	0.074
r_ncsr_local_group_5	0.069
r_symmetry_nbtor_other	0.066
r_bond_other_d	0.035
r_gen_planes_other	0.011
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16161
Nucleic Acid Atoms
Solvent Atoms	1517
Heterogen Atoms	63

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building