8VLH | pdb_00008vlh

Crystal structure of Ash1L PHD-BAH domains

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4L58	4L58 and 1W4S
experimental model	PDB	1W4S	4L58 and 1W4S

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.1 M Bis-Tris propane pH 10, 0.25 M strontium chloride, 0.01 M ammonium sulfate, and 25% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 173.11	α = 90
b = 60.575	β = 97.92
c = 53.588	γ = 90

Symmetry
Space Group	C 1 2 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 PILATUS 200K		2020-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5419

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.4	48.2	97	0.063	0.077	0.996	12.2	2.8		20953

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49			0.319	0.429	0.841	2.3

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	4L58 and 1W4S	2.403	48.2	20951	1062	96.852	0.233	0.2298	0.2302	0.2845	0.2836	43.147

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]
2.487		0.021	-0.082		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.737
r_dihedral_angle_3_deg	15.32
r_dihedral_angle_4_deg	11.906
r_dihedral_angle_1_deg	6.001
r_angle_refined_deg	0.736
r_nbtor_refined	0.303
r_symmetry_nbd_refined	0.184
r_nbd_refined	0.176
r_symmetry_xyhbond_nbd_refined	0.129
r_xyhbond_nbd_refined	0.113
r_chiral_restr	0.064
r_bond_refined_d	0.002
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4101
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MrBUMP	phasing