6PGC | pdb_00006pgc

WDR5delta32 bound to methyl benzyl(4-(4-(hydroxymethyl)-1H-imidazol-2-yl)butyl)carbamate

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	0.237 M ammonium sulfate, 0.1 M Bis-Tris chloride, pH 6.92, 25.7% w/v MPEG5000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.716	α = 90
b = 65.285	β = 90
c = 97.173	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	1.81	46.72	99.2	0.999	17.1	7.2		27580

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	1.81	1.85	87		0.791	2.6	7.1

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 6PG4	1.81	42.14	26139	1383	99.7	0.20529	0.20302	0.2477	RANDOM	21.431

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]
-0.16			-1.47		1.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.968
r_dihedral_angle_4_deg	25.764
r_dihedral_angle_3_deg	13.082
r_dihedral_angle_1_deg	8.09
r_long_range_B_refined	3.864
r_long_range_B_other	3.864
r_scangle_other	2.423
r_angle_other_deg	2.354
r_mcangle_it	2.153
r_mcangle_other	2.152
r_scbond_it	1.557
r_scbond_other	1.556
r_angle_refined_deg	1.437
r_mcbond_it	1.382
r_mcbond_other	1.382
r_chiral_restr	0.061
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	200
Heterogen Atoms	33

Software

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