3K3N

Crystal structure of the catalytic core domain of human PHF8

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	200mM KCl, 100mM Mes, 20% PEG5K, pH 6.5, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.238	α = 90
b = 52.583	β = 90
c = 134.93	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	200	CCD	MARMOSAIC 225 mm CCD		2009-05-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.97939	SSRF	BL17U

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	50	98	0.055	0.06	31	5.7	15300	14988	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	4.1		0.426	0.37	2.6	3.7	616

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2YU2	2.4	20	14861	14109	752	98.32	0.224	0.222	0.261	RANDOM	33.634

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]
2.17			-0.41		-1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.369
r_dihedral_angle_4_deg	17.318
r_dihedral_angle_3_deg	15.909
r_dihedral_angle_1_deg	5.328
r_scangle_it	1.318
r_angle_refined_deg	1.019
r_scbond_it	0.807
r_mcangle_it	0.617
r_mcbond_it	0.329
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2648
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling