5UPD

Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OOI	pdb entry 3OOI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	20% PEG-5000-MME, 0.1 M bis-tris, 0.02 M sarcosine

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.16	α = 90
b = 62.81	β = 109.78
c = 48.84	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX-300		2015-01-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97957	CLSI	08ID-1

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	1.8	41.55	98.9	0.105	0.124	0.064	0.995	11.1	3.7		23067

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	1.8	1.85	96.2		0.714	0.859	0.471	0.626		3.2	1678

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3OOI	1.8	41.55	21949	1118	98.79	0.1856	0.1839	0.2182	24.398

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]
1.35		0.47	-0.52		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.055
r_dihedral_angle_4_deg	21.717
r_dihedral_angle_3_deg	13.356
r_dihedral_angle_1_deg	6.008
r_mcangle_it	3.416
r_mcbond_it	2.221
r_mcbond_other	2.221
r_angle_refined_deg	1.801
r_angle_other_deg	1.033
r_chiral_restr	0.109

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.055
r_dihedral_angle_4_deg	21.717
r_dihedral_angle_3_deg	13.356
r_dihedral_angle_1_deg	6.008
r_mcangle_it	3.416
r_mcbond_it	2.221
r_mcbond_other	2.221
r_angle_refined_deg	1.801
r_angle_other_deg	1.033
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1644
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	47

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.