9QN5 | pdb_00009qn5

Crystal structure of human SUMO E1 with small unit cell parameters in the P1 21 1 space group.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XOG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	25% PEG 3350, 0.8M ammonium acetate, 100mM MES pH 6.5, 10mM ATP, 10mM magnesium chloride, 10mM TCEP, 2.5% PEG 400, 1mM ESO-25.

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.47	α = 90
b = 115.562	β = 104.7
c = 98.571	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS3 2M		2023-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.88560	ESRF	ID23-1

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	1.968	73.544	96.3	0.998	7.6	3.4		135032			36.94

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	1.968	2.002			0.369

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.97	73.54	127152	6555	95.35	0.20113	0.19889	0.2068	0.24392	0.2476	RANDOM	52.366

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]
0.26		1.07	-2.54		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.476
r_long_range_B_other	10.198
r_long_range_B_refined	10.196
r_scangle_other	8.249
r_dihedral_angle_2_deg	7.693
r_dihedral_angle_1_deg	6.373
r_mcangle_it	6.373
r_mcangle_other	6.373
r_scbond_it	5.462
r_scbond_other	5.461
r_mcbond_it	4.51
r_mcbond_other	4.51
r_angle_refined_deg	1.573
r_angle_other_deg	0.53
r_chiral_restr	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12903
Nucleic Acid Atoms
Solvent Atoms	176
Heterogen Atoms	66

Software

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