9EKP | pdb_00009ekp

Crystal structure of WDR55 in complex with XS381774

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7KQQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	10% w/v PEG2000, 20% v/v ethylene glycol, 0.02M of each amino acid, 0.1M bicine/Trizma base pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.89	57.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.316	α = 90
b = 58.412	β = 96.29
c = 87.218	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	CCD	RIGAKU SATURN A200		2024-06-25		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54

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	1.95	34.83	97.5	0.082	0.091	0.041	0.998	14.1	4.9		55823

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	1.95	2		95.9	0.685	0.764	0.335	0.774		5

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	1.95	34.83	53046	2744	97.16	0.15825	0.15578	0.1699	0.20584	0.2109	RANDOM	28.458

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]
-0.55		0.28	-0.12		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	13.879
r_long_range_B_other	13.314
r_dihedral_angle_3_deg	11.717
r_scangle_other	8.863
r_mcangle_other	7.901
r_mcangle_it	7.9
r_dihedral_angle_1_deg	7.454
r_dihedral_angle_2_deg	5.978
r_scbond_it	5.728
r_scbond_other	5.727
r_mcbond_it	5.132
r_mcbond_other	5.123
r_rigid_bond_restr	2.415
r_angle_refined_deg	1.289
r_angle_other_deg	0.455
r_chiral_restr	0.059
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4714
Nucleic Acid Atoms
Solvent Atoms	336
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing