6PGB | pdb_00006pgb

WDR5delta32 bound to N-(4-(5-(hydroxymethyl)-1H-imidazol-2-yl)butyl)-2-phenylacetamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6PG4	PDB entry 6PG4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		281	0.101 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 5.63, 25.8% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.798	α = 90
b = 65.275	β = 90
c = 97.127	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	CCD	ADSC QUANTUM 315r		2016-11-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95370	Australian Synchrotron	MX2

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	1.73	48.56	98.1	0.996	12.6	13.6		31184

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	1.73	1.76	80		0.862	2.8

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 (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	PDB entry 6PG4	1.73	48.56	29595	1534	97.86	0.17612	0.174	0.18	0.21697	0.23	RANDOM	10.552

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]
-0.71			-0.79		1.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.48
r_dihedral_angle_4_deg	22.107
r_dihedral_angle_3_deg	13.39
r_dihedral_angle_1_deg	8.575
r_long_range_B_refined	4.47
r_long_range_B_other	4.469
r_angle_other_deg	2.35
r_scangle_other	1.578
r_angle_refined_deg	1.407
r_mcangle_it	1.331
r_mcangle_other	1.33
r_scbond_it	0.974
r_scbond_other	0.947
r_mcbond_it	0.764
r_mcbond_other	0.763
r_chiral_restr	0.065
r_bond_other_d	0.036
r_bond_refined_d	0.009
r_gen_planes_other	0.009
r_gen_planes_refined	0.007
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	2360
Nucleic Acid Atoms
Solvent Atoms	352
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing