6WAV

Crystal structure of PHF1 in complex with H3K36me3 substitution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	291	1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 153.003	α = 90
b = 65.616	β = 97.122
c = 29.026	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	CCD	RIGAKU SATURN A200		2016-06-08	M	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	1.7	40.07	93.8	0.048	0.056	0.029	0.998	16.4	3.7		29381

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	1.7	1.73	90.9		0.416	0.487	0.251	0.81		3.6

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4HCZ	1.7	32.802	29359	1455	93.42	0.199	0.197	0.2407	18.886

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]
0.098		0.025	0.766		-0.844

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.638
r_dihedral_angle_4_deg	13.449
r_dihedral_angle_3_deg	12.48
r_dihedral_angle_1_deg	7.147
r_lrange_it	4.533
r_lrange_other	4.423
r_scangle_other	3.17
r_scangle_it	3.166
r_mcangle_other	2.585
r_mcangle_it	2.584
r_scbond_it	2.106
r_scbond_other	2.092
r_mcbond_it	1.708
r_mcbond_other	1.703
r_angle_refined_deg	1.664
r_angle_other_deg	1.305
r_symmetry_nbd_refined	0.305
r_nbd_refined	0.228
r_nbd_other	0.201
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.149
r_xyhbond_nbd_refined	0.145
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.064
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2152
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	49

Software

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